Yeah transferring animations can be a bit pain in the ass sometimes...
Remember that both models need to be in .mdl form to work.
Usually the problem is that the first unit has a bone and the second one has a helper with the same name.
Bones and helpers are almost the same thing, except helpers can't store information so when you transfer an animation, the helper get's information and the model gets bugged.
If this is the problem, you have to open the models in a note pad and change every "helper" word to "bone" (except the very first word, which is "NumHelpers") then you will need to set the number of "NumBones" to NumBones + NumHelpers and the number of "NumHelpers" to 0)
Another problem can be (like Werewulf said) that the bones have different names. In this case no information is transferred and you need to rename the bones to have the same name or find another model with the needed animations...
I hope this helped...