T Rex arms will definitely make it hard to fish. Lol just kidding. I had a few issues at first also. Best advice my dad always gave me if it feels like a hit set the hook. If it turns out it was a tree oh well. A quick snappy hook set usually get them and I keep the rod tip a little lower also. If the rod is at 10 o'clock. There's not much left to set the hook and you have to wind down then set it giving the fish time to spit it out. Keep the rod tip about 3 o'clock and just let it rip when ya get a hit. With braids and stiff rods you'll also pull more hooks out. Something has to give. I use braids on rods with more give and mono on stiffer rods.

that bass section is a different breed, ... mongoloids I tell ya!

The motion you are using when setting the hook may have changed when you sit down in the Yak. You may be putting the same effort and timing in your set but you may just be moving your hands and not your rod tip enough to get that hook moving with enough power at the very beginning of your set.
I had to work on this issue when I first started fish-N from the Yak.

You don't need long arms to have an effective hookset. It's not so much the use of the arms as it is the wrist and bending at the elbows. Lock you're elbows to your side and bend the elbows and wrist.
A lot of you may laugh, but get a film of how Bill Dance and watch how he sets the hook.
Fishing out of a kayak or boat makes no difference in hook set if you have a good solid technique.
http://www.youtube.com/watch?v=hCEGLliuZhg

If you don't have the problem from the boat then like others have mentioned its probably the wind. Unless you're using two anchors or there is no wind, you'll be making some weird angled hook sets from a kayak with more slack in line from bow turning on you. With the time of year (spring), cold fronts every weekend making the bite tough, the usual winds, expect it. I've noticed it as well.