I've been having similar problems (disappearing action buttons, very fast timeouts when trying to join a table). My problem has been happening without running MTH or AHK. The only thing I've had running were allSnap and PokerAceHUD.
I'd been searching around on the web to see if there were any solutions and came across
this. It "says" that it is a graphics card acceleration problem. The first time I tried this fix, it worked. But hasn't worked since then.
Just as a point of reference I'm running Windows 2000 and have an Asus A9550 graphics card. I'd been thinking that this may be a graphics card problem since I just got this card. Or possibly something specific to Windows 2K. But after reading this thread, I'm not so sure. Anyone having this problem with Windows XP?