I have a suggestion that might help with a little back story as well.
Try using a small drill bit that can cut a relief hole prior to milling the pocket, that is, if the pocket is something like a hole. By removing the center of the pocket with a drill takes away added stress to the endmill when plunging into a hole.
I have had these some problems while machining metal in the machine shop. To fix this issue, I would run a smaller relief cut into the hole and then follow it with the desired diameter cutter.
The problem it sounds like to me is that the feed is one of the problems. If this is the case, just slow it down a bit to see if that works. Even cutting the feedrate down by 50% would give you an idea if it is enough. Also, length of endmills do play a role if the tool is long sticking out of the collet. The further out it is the more likely you will have tool deflection.
In a plunge cut, deflection can become exaggerated because of the pressures that are pushed upon the tip of the endmill. If you are cutting the small pocket where the endmill is not moving that far from the centerline of the hole, then material buildup can be a problem. I know you tried different types of cutters and they still didnt work.
With a belt driven machine, you say you have heard the thud as if the machine has bottomed out, that sounds like a belt jumping teeth. You checked all belts and V guides and say they are good. So, the only other thing is possible is that you are pushing the machine too hard and the return force against the drive motors as the machine tries to cut compounds the faster, or deeper you go into the cut per pass.
I know this is a bit long winded, but I would be reducing the feed of my machine and/or running a relief cut moving forward. By process of elimination, you should have found the problem if it was in the machine’s hardware, (belts, guides, motors, spindle collets, etc.). Now if its not any of these, then you look into the program, (depth of cut, type of cut, feed rates, spindle speeds, etc.).
Hope you figure this out and you touch base back with us to give us the good news of it being fixed and what the issue was. Good luck.