Photoshop: Merging layers ignores certain blending modes and layer styles! Saving too!!

So, I have an layer in the bottom, which is completely opaque and doesn't have any blending modes or anything. I have a layer (or more) or top, witch happen to have some blending modes and layer styles applied. I merge the whole thing and POOF... The final result looks completely different. Merging ignored some of the layer styles and blending modes.
The same thing sometimes happens when saving images!!!!
How the heck did this pass QA? Please fix!