Although i'm using the current Beta 1 of JoComment (native for Joomla 1.5), I also use JoomlaPack for a similar task as you - for a localhost<>livesite deployment system.
I have encountered a few problems with JoomlaPack restoring incorrect permissions no matter what I did - various random things on my restored site would be glitched up or just not work at all. I would suggest to use JoomlaPack in this way as it proved to be 100% error proof so far (for me):
1) Backup your site using either ZIP or JPA, doesn't matter
2) On the target site, ERASE the entire public_html folder (or in the case of XAMPP, the entire htdocs folder) to wipe your target webhost. This is important as the JoomlaPack "restore" will usually not overwrite certain files (PHP problem)
3) Upload the .ZIP or .JPA archive to your target webhost root, along with JoomlaPack's kickstart.php, and rename your .htaccess file to disable it
4) Run kickstart.php and select "FTP Extract Method" and DO NOT check the 'Restore Permissions' option < many webhosts (including my own HostGator, apaprently GoDaddy does it too) seem to not preserve the permissions correctly.
5) Fill out the FTP details of a root user. I use the same details that I have set up for my "Joomla FTP Layer" (from Global Configuration), works well. Continue with the Kickstart restore as normal.
6) If restoring on a Linux server, be sure to re-assign all your file/folder permissions for higher security before going live. Via SSH you can do it with:
find . -type f -exec chmod 644 {} ;
find . -type d -exec chmod 755 {} ;
...you can also do it with a quality FTP client such as FlashFXP or SmartFTP - the former allows a recursive CHMOD, the latter supports a "Find all Files"/"Find All Folders" > CHMOD kind of option.
Infact, it might just be permissions. Make sure all your files are 0644 and all your dirs are 0755. JoomlaPack does wierd things with permissions.