Looks like there is a new bug with Gunslingers nor crouching into cover. The screen will go up but your toon will stay standing and you can't use your cover abilities.
This is the Dev response:
Originally Posted by SWTOR
Hi folks, thanks for reporting this. We've confirmed and added this to our list of Known Issues and we are now working on a fix for an upcoming patch. Apologies for the inconvenience and thank you for your patience.
(Source)
Also this is the suggested work around:
Originally Posted by SWTOR
Workaround: If players are not moving, Portable Cover works properly with a single activation of Take Cover. Furthermore, players who drop their Portable Cover while moving can activate the ability again to move into cover.
(source)