I'm not a Novice to Partition Wizard and have used it often.
However, I used for the first time the other day on my OS (Boot,...) partition to shrink it to a size able to accommodate an SSD. Sorry to say it moved files and screwed up! The MFT wasn't the issue.
I recovered from an image and completed the job. But take WHS's advice early in the thread and basically be prepared to recover from a PW foul up.
Also, if you ever invoke your factory recovery you'll be back to the old partition structure.
Did you use the PW CD? While
we´ve had failures using PW installed version which must commit to RAM at reboot to complete tasks, I recall no failure reported in thousands of cases where PW CD has been used here to do both simple and complicated partitioning operations.
Please document thoroughly with screenshots any PW boot disk failures, as
non-specific comments disparaging the most important tool we use here are not helpful and confuse the OP.