In:
"C:\Program Files (x86)\Steam\steamapps\Star Trek Online\Live\piggs"
and
"C:\Program Files (x86)\Steam\steamapps\common\star trek online\Star Trek Online\Live\piggs"

I wonder how that could happen.

Ok, something VERY very strange is going on now:

"C:\Program Files (x86)\Steam\steamapps\common\star trek online\Star Trek Online\Live\piggs\Star Trek Online\Live\piggs"

just appeared.