I am having this same EXACT issue with my Kingston HyperX SSD as seen in this thread:
https://forums.macrumors.com/threads/1213115/
And even before I enabled TRIM it was doing this (which is why I enabled it, thinking it would help). Although I'm not having any issues with getting good speed (as I have 6gb/s negotiated speed on the HDD bay, but unfortunately only 3gb/s on the Optibay

), it sucks having to wait for the beach balls to go away...
Which is why I think this problem is an OS X problem, because I'm having no problem with Boot Camp!
500 MB/s+ read, about 420+ write!!!

But MAN is it flaky as hell on OS X!