I can't explain your trouble in detail, but it is possible
that part of it comes from the fact that the MBR partition
ID has changed to 169 (0xa9) in the meantime.
"sysinst" doesn't know much about this yet. While the
new kernels and utilities still accept the 165 partition ID if
already present, the freshly generated entries are 169
per default. Perhaps this confuses "sysinst".

I can only recommend to run "fdisk" and "disklabel" manually
and to make sure you get it consistent.

best regards
Matthias