Alignment Tool on Dell Mini 9

I recently upgraded a Mini 9 to a 32gb SuperTalent SSD. I backed up the original drive using Paragon Backup & Recovery. When I install the image (2 partitions) on the new 32gb drive everything is fine, however, after aligning with PAT 2.0 I get never-ending boot errors. NTOSKRNL is missing or corrupt, HAL.DLL is missing or corrupt. Chkdsk finds and fixes errors, but doesn't fix the booting problem. I've checked the boot.ini settings, and I've re-created the image without the Dell utility partition - but nothing works after aligning!
It's as if the system files are all corrupted by the alignment operation.

Any thoughts on what might be my problem?

Thanks

 

is it working ok without it being aligned using PAT? If you ran chkdsk does it find and fix errors before aligning? If you align only 1 partition does the error occur still? It might be that you drive does not like PAT

 

The computer boots and works fine before Aligning (both two partition & single partition). Occasionally, the system freezes momentarily. I've read this might be due to partition alignment (might also be the slower cpu).

I ran PAT and it showed the alignment to be non-optimal. However, aligning always breaks the booting process (whether two partitions or single partition).

Unfortunately, the PC didn't come with a recovery disk (or I lost it). I tried using my XP Pro disk to repair, but it doesn't recognize the XP home installation for repairing purposes.

Thanks