Microwaved eggs was probably one of the first things that I learned to cook -- I don't know I'd consider it an 'omlette' necessarily -- it was just a bowl, oiled, broke an egg in it, a touch of milk or water, mixed, and then microwaved.
When you're rushing to get out the door in the morning, it's a dead simple breakfast; I was recently out of town, and the place I was getting my breakfast in the morning (a bagel joint) did basically the same thing -- put a laddle of egg into a container, microwaved, put it on the bagel, and you were out the door.
Personally, I'm of the opinion that velvetta melts at a low enough temp that if you're using the pre-sliced stuff, you'd probably be okay just cooking the egg, putting the cheese-food on it, leave it in the microwave (off) for ~30 sec, and it'll have started to melt.
(but then again, I like to know cheese is there ... not be some runny molten filling that runs out when you're eating something, so I don't want it too melted)
Sunflower lecithin (sorry, best link I could find) is gaining in popularity as an alternative to soy lecithin because it is widely perceived to have a neutral taste and actually has superior emulsifying properties. It's a little on the expensive side, though.
Soy lecithin by itself doesn't taste horrible if you buy it as a food additive (as opposed to a nutritional supplement). It's common to find in a lot of popular frozen pasta-and-sauce dishes, such as Michelina's, which obviously must be microwaveable without the sauce curdling or separating.
Another option is Sodium Stearoyl Lactylate, if you can get hold of it. This one adds a little sweetness which is generally pleasant-tasting, or at least inoffensive. You'll find it used most often as a dough conditioner or in baked goods, but another popular use for it is in commercial sauces, although unfortunately I can't find specific examples right now.
But probably the best emulsifier for what you're trying to do here is xanthan gum. It's also used as a gelling agent, but in small quantities works as just an emulsifier. You can find it, for example, in this Bertolli Creamy Alfredo Pasta Sauce - exactly the sort of thing you're making. It's also used in the Stouffer's Alfredo sauce.
Mix in a little lecithin or xanthan gum as an emulsifier while the sauce is fresh or cooking and it's very unlikely that your sauce will separate, either in the fridge or in the microwave.
As for what you can do to specifically prevent separation while reheating, if you didn't add any emulsifiers in the first place... I really don't think there's anything you can do. If you're a slow enough eater the sauce will eventually separate right in front of you; that's just what happens when you have water and fat in the same sauce. Best to reheat on the stove top in that case, and stir frequently to prevent any further separation.
Best Answer
Three possible things to consider: steam in the electronics (which should be sealed from that so it would be likely to happen again); sparking when heating the last item, which can confuse the electronics; simple overheating, again of the electronics.
In the latter two cases, leaving it unplugged for a few minutes before trying again should be fine. This is less likely to help if the control circuit has got wet. I assume here that you've got a sensible electrical system with an independent safety earth (ground) and circuit breakers, like I'm familiar with testing appliances on. If you don't, I can't recommend that you test it. I don't suggest that you remove any covers, and definitely don't open it up without it having been unplugged for several hours, or power it up with any covers off, even if you'd do this on other appliances.