Some assets from SWC are not imported in Flash Builder

Some assets from SWC are not imported in Flash Builder

For almost all of my projects I export visual assets from Flash Pro to SWC
to then import them in Flash Builder. Today I stumbled across a really
bothersome problem.
Some of my assets are not being imported. I've tried clearing my projects
multiple times, restarting my Flash Builder IDE, re-exporting my SWC.
Clearly there's a problem when importing it, because when I decompiled my
SWC/library.swf, I saw that all of my assets are exported just fine. When
I decompile my output SWF I see that instead of some assets there is a red
rectangle, and some of them are just invisible.
I don't know what to think and can't figure it out. The only thing that
might be a case is the file size of the SWC (approximately 2.5 MB), and
there are almost 160 linkages in there.
I wasn't able to find anything on the internet regarding the file size
limit or anything like that.
I'm using Flash Pro CC and Flash Builder 4.7 Standard on a Mac OS X 10.8.4
These are the red boxes I'm talking about: