Did you see the "ACK" message as well as the flight plan.
From my experience, you may be given the "flight plan" that ops have sublitted to the system. What ops may not tell you is that they received a REJ or MAN message and subsequently changed the flight plan to a more reasonable one in order to obtain an ACK.
There could also be an ops guy that with the old avoid slots tunnel vision, puts you at low levels or on massive de-tours and makes no allowance for the extra time and or fuel that it is going to cost!
However, what you can do is visit the CFMU website and put your dodgy plan into the structured editor and see what the system says.
Regards,
DFC