Am I the only one with this problem?
No.

So this is odd... I tried this and the basic bottle (grey colored in the library) can change colors no problems. When I added one of the pre-colored ones, it showed up properly. But when I tried to recolor it, it turned dark grey. Now all of the pre-colored ones are dark grey for me and I can't change them back or to anything else. However, I can still recolor the basic bottle.

It will be fixed when the part is converted to newer version of part system.

@B1Trash, I'm having the same problem. Did you ever find a way to return to the default coloring on the pre-coloured flasks? Closing & reopening or a new file for instance? (So far I've had no joy...)

They spawn in dark grey for me right now.

Thanks. I was hoping it was one of those things where if you only perform the right esoteric series of movements, suddenly it reverts.

Ha!