This is a pretty murky story. My take is, if chkdsk reports a problem, then there is a problem.
And why did you move the recovery partition to the SSD. Is that a Dell system where the bootmgr is on the recovery partition? If yes, the bootmgr should be moved to C.
An unaligned SSD is not good, regardless which partition is first.
Before we proceed, I suggest you post a picture of your Disk Management of the SSD so that we can see what's going on.