Paragon Alignment Tool 2.0 problem

I am running Win7 Ultimate 64.
I ran PAT 2.0. It said one of my drives needed alignment.
I selected that drive and it said that Windows would need to reboot.
Windows rebooted and PAT ran a DOS screen which started with about 7 blue dashes. Then another screen came up, displayed several things like checking file integrity, etc. Then it rebooted and came right back to the same DOS screen. This reboot process continued about 6 times til I got frustrated and escaped out of the problem. Tried to boot into Windows and instead got this DOS screen over and over. Finally escaped out, shut down the computer, unplugged the power cord, hit the power button, rebooted, and I got the windows dos screen about windows not starting correctly. I selected "start windows normally" and back came the PAT dos screen again. ARG!
Finally ran system restore, got rid of PAT, but now every time I boot Windows, after the BIOS but before Windows starts, I get the blue dashes. It also takes longer to boot up. Is there a remnant of this PAT left behind somehow and how do I get rid of it!!! It's been fairly frustrating.

 

Looks like it's set in MBR. You can do "Update MBR" from Paragon CD or "fixmbr" command from Windows CD.

 

to remove blue dashes:
1) Click on Start, Run and type MSCONFIG and press Enter
2) Click on the BOOT.INI tab
3) Un-check the NOGUIBOOT checkbox and click OK
4) Reboot the computer

By the way: warning that alignment is not completed allows to continue alignment and avoid data loss because of accident power off or restart.
To remove the warning you need to perform Update MBR (or fixmbr as suggested by knot)

As of longer boot time: it was better to complete alignment. I think the reason is that partition start\end is changed, but its not correctly updated somewhere in Windows.

 

Thanks, Mech_An and Knot! That did it, the GUI boot box was checked.
Now the only problem is, why did PAT get into a loop?
The drive I was aligning was an internal drive, but I do have a USB drive connected to the computer? Maybe I should disconnect it while PAT is working?

 

It appears that alignment was not completed due to file system errors found.
Then you did hard reset & PAT created MBR entry which allows to continue alignemnt because of accidental power loss.

I don't think that USB-drive could prevent alignment. More likely that there are file system errors on the partition you want to align.

I would recommend you the following:
* open Start -Run and type CMD
right-click found cmd.exe and select Run As Administrator
* in the Command prompt type:
chkdsk c: /f
press Enter
* This operation require restart. Schedule it to run before next system start and restart your PC.
Repeat this operation for all partitions on internal hard drive.

Then you can try to run alignment again.

Note: It is more safe to create backup of the source HDD before running alignment tool.