Yes. sometimes very different training cultures. Usually however, the merged airlines pick one set of ops specs, because combining the two would create a new set of ops specs that would have to be re-certified (Big $$$).
In the case of AA/TWA, TWA had to come over to our side (unfortunately). TWA guys got some ground school and sim about 4-5 days worth I think. AA guys got about 6 hours of ground school on differences.
Your right about it being a major concern in a merger, but one that is often overlooked because the only people interested in a merger are investment bankers and a handful of stockholders--senior management. These players are only looking for the big payout in the short term, Stephen Wolf is a perfect example of this kind of behavior.