I may have a unique problem, or maybe I was stupid and changed a small detail that left me with this problem (although I am pretty sure I did not):
I have a layer with several masks on it and a stroke effect, which is animated over time. Also, I have some lights with lens flares attached, the whole thing is animated to "write" text on the screen with the lens flares.
To make the text glow, I added an adjustment layer between the stroke layer (bottom) and the lights (top), so just the text would glow, not the lights. I added a black solid as a BG, otherwise the glow won't work later on.
I then pre-composed this, brought it into another composition (comp2) and stretched the time on the pre-comp to make it slower.
Finally, I used this comp2 in my main composition, which includes some particular effects etc.
I rendered this thing several times yesterday, it worked very well. All of a sudden, about 1 day later, the glow does not show anymore, in the final composition the stroked text is even shown a little bit darker. When I went through the comps, even comp2 renders without the glow and a darker text now. BUT comp2 SHOWS with the glow in AE Navigator - how can this be? In fact, only in the last comp, the glow is also gone in AE navigator...
I am seriously stumped. I have no idea why this is happening, even earlier versions of the file have this problem now.