A good way to test what the real issue is, is to use a fairly large map and as soon as you spot invisible spawn, have your PC quaff an invisibility potion. Then move to a point as far away from the spawned creatures as you can to get out of their perception ranges. When you then reapproach them after a few moments, you should now see them.
In a DM'd module, a DM porting NPCs to the far corner of a map, then porting them back after a moment fixes them. Limboing a creature and calling it back is another fix. This is also why, several folk that change a NPCs appearance after it spawns in also script the NPCs to port and return or apply various other delayed effects to force an appearance update to be sent to clients.
The appearance data is sent from the server to the client (doesn't matter if both are the same) when a creature spawns in and whenever they again come into perception range if applicable after. The appearance data can be dropped/lost/aborted however when that creature's combat AIs kick in. So spawning them well in advance is usually the easiest cure. Conditions causing lag can also delay the data before combat begins, which also interupts the update of appearances.
From my own testing I've found little difference in using Bioware vs CEP or other custom custom appearances. Its when I add customized weapons and other items that the issues appear. Dynamic models often suffer the most as they not only have a base appearance, but additional data for each visible part needs sent as well. Since I use customized Dynamic Half Orcs, Gnomes and Halflings in my work to create detailed Orcs, Goblins and Kobolds, I have to follow my recomendations listed previously to avoid the invisible creatures. Even then, if there are other lag issues or some knucklehead "runs" through an area spawning several mobs back to back ... they can crop up.
'> So Area Cleaners, limiting Heartbeats, better and more efficient AIs and numerous other "good" building practices are all a neccessary part of having a smooth running module and avoiding this annoying glitch.