Well, one good reason is that the commercial solutions are one-size-fits all, and thus often fit no one.
I've seen serious trouble at Lucent Technologies and Oxford University after they brought in commercial systems to replace in-house systems. In both cases, we found that the commercial systems really weren't well adapted to the needs of the business. One gets stuck with a system that isn't quite right, and that cannot practically be customized. Large amounts of staff time were spend in training for and dealing with these systems.
The point is that all these systems are designed for bog-standard companies. If your company matches the software, then you may be OK. But, if your company doesn't match the software, then *you* will have to make painful adjustments. The software won't.
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