As a system it does the job it's supposed to do, although the interface isn't very intuitive or user friendly. As part of the changes in allowances and payment mechanisms the loggies should really have spent some time coming up with meaningful names for things.
The requirement to cater for users outside fixed sites in the UK should have been built in from the start, not added as an afterthought.
Pay cock ups happen, they always have done and they will continue to do so until people are taken out of the equation. In the past it was blamed on other things, JPA is a convenient excuse now for the same people who cocked up paper based systems before.
Personally I've had no real issues with it, other than the time taken to work out how the interface actually worked.