The channels problem affects some systems with the latest maintenance releases of 4.0 and 4.1, but as said there are patch/private builds for both. In fact codewise 4.0 and 4.1 are very close kissing cousins - a bug in one is very likely to also exist in the other and by the same virtue the fix is one is usually mirrored by a fix in the other. So there is little to choose between the latest 4.0 and 4.1, so go for 4.1 to get the extra features.
The VMPro change is a hoot. It was a bug but one thats been around for so long it had pretty well become accepted operation, except they've now fixed it and so confused everyone again.