The Ioun Stone comes from Jack Vance's Dying Earth series, which is where the "fire and forget" spell casting of D&D came from too, as well as some of the spells such as prismatic spray. The stones are harvested from the core of neutron stars that are being sliced away by the Nothing at the edge of the universe and are therefore rare and difficult to obtain. Their origin is dealt with in the story "Morreion" in the collection Rhialto the Marvelous.
They were introduced in The Strategic Review, Vol. 1, No. 4, p. 10 (Winter 1975; no author given, although there is a reference to Vance approving the design/inclusion and I know he and Gygax corresponded) and first made their way into the rulebooks with the original DMG, as far as I can see.
By strict RAW, it would seem that the ioun stone grants all the benefits of the ring, except with a lower healing rate.
This stone grants the wearer the ability to regenerate 1 point of damage per 10 minutes. Regeneration works like a ring of regeneration. It only cures damage taken while the character is using the stone.
Contextually, "works like a ring of regeneration", with no colon- or dash-separated clause to restrict it, does in fact include everything. The following sentence restates the key limitation for clarity and rephrases it to apply to the stone instead of the original ring (which wouldn't make any sense).
While the normal rationale for the immunity to bleeding damage that the ring gives can be thought of as a logical outcome of the constant healing, it's given as its own feature, so it applies without regard for order of operations or any other exceptions: the wearer is not merely cured of any bleeding at the start of each turn, but cannot take any damage from that. As such, it still applies the same way to the ioun stone, even though the stone does not heal nearly as often. (This can be justified in fluff as simply being such a slow constant healing that it only adds up to a single point every ten minutes, but in any case the RAW seems clear enough.)
From a standpoint of balance, which is certainly not a standpoint of RAW but can at least inform houserules, the ioun stone's additional abilities are not nearly so imbalanced as one might think. Bleed damage is not unheard of, but neither is it all that common, and limb removal does not, as far as I know, actually have any rules to enable it. So charging 20,000gp instead of 90,000gp for 1/100 the healing rate isn't too cheap. If anything, it's really not that great a bargain, and the original ring cost a pretty penny anyway.
Best Answer
This GM would rule that if two or more otherwise identical ioun stones grant bonuses on different rolls or to different values, a creature can gain the benefit of each otherwise identical ioun stone.
For example, this GM would have no difficulty ruling that a creature that sends spinning both an ioun stone (dusty rose prism) and an ioun stone (cracked dusty rose prism) then benefits from both the first stone's +1 insight bonus to AC and the second stone's +1 competence bonus on initiative checks.
Likewise, this GM would rule that the same creature can benefit both from an ioun stone (cracked pale green prism) that grants a +1 competence bonus on attack rolls and from an ioun stone (cracked pale green prism) that grants a +1 competence bonus on saving throws. Bonuses on or to different things that are from different sources generally stack, and in this case the sources are two different ioun stones, each having a different effect.
However, a stricter GM may want to apply the rules for Combining Magic Effects on Stacking Effects on Same Effect with Differing Results (noting, however, that such rules are usually applied in the context of spell effects) and declare the two identical ioun stones the same effect (for example, two ioun stones (cracked pale green prisms)) with differing results (for example, a bonus on attack rolls and a bonus on saving throws). Such a ruling would mean the creature benefits only from the last-sent-spinning otherwise identical ioun stone. This GM does not endorse such a ruling, but such a ruling wouldn't cause this player to abandon a campaign.
(Also, because the text on d20PFSRD is slightly incomplete, "For stones that have multiple possible effects…, the exact effect is determined by the item crafter when it is created and cannot be changed thereafter" (Seekers of Secrets 46). Thus, for example, it's not like a creature that finds an ioun stone (cracked pale green prism) and sends the stone spinning around its head itself picks the bonus; instead, the stone's creator picked the bonus when the stone was created.)
In Dungeons and Dragons
I found nothing like your DM's recollection of the limit on ioun stones in the Dungeon Master's Guide for AD&D, 2e, 3e, or 3.5e. Also silent is the Encyclopedia Magica for AD&D 2E (the game's largest magic item collection so far) in its entry on Ioun Stones (613-8). (Right after Internal Conjuration Engine but before Ipsissimo's Black Goose.)
Further, Hargenrader's Dragon #174 (Oct. 1991) Bazaar of the Bizarre column "Ioun Stones: Where Do You Go If You Want Some More?" (90-4) references the Polyhedron #15 Dispel Confusion column that seems to indicate ioun stones can increase an AD&D 2e character's ability scores not only above their racial maxima but also even above 18! Despite mentioning this unusual effect, Hargenrader's article doesn't discuss—rather surprisingly, in retrospect—the possibility of a creature employing several identical stones. (However, given the frequently punitive nature of old school D&D, this reader expects any attempt to send multiple identical stones spinning to yield explosions.)
Finally, the Encyclopedia Magica lists ioun stones as possibly either burnt out, normal, supercharged, or cursed. Inferior stones—cracked, flawed, and scorched—and resonating stones are, presumably, a Pathfinder invention so any information about a creature specifically being unable to use simultaneously both a typical stone and an otherwise identical inferior stone would have to buried even deeper within one of Pathfinder's multitudinous supplements.
Note: I also looked at Pelgrane Press's Primer of Practical Magic (2004). The book is billed as "Spells and artifacts from the Dying Earth, made available for use in [the] d20" System, and includes fifty or so additional ioun stones (some underpriced, some unbalanced, and others both—introduce them cautiously to a campaign!), but that text, too, says nothing about multiples or identicals.