The CompoJoom !JoomlaComment component has never had any issues with Joomla's default SEF generation for me as long as I've been here (since 4.0 alpha 3), with the exception of a couple of links using raw URI with non-SEF (but still working).
My best suggestion is this:
(1) Enable Joomla SEF and mod_rewrite
(2) FULL Uninstall both commenting components
(3) Clear the Joomla cache for backend and frontend, as well as browser cache
(4) Enable the original .htaccess that comes with Joomla 1.5.15 (or leave it as htaccess.txt if it's on a XAMPP for Windows install)
(5) Ensure every aspect of the Joomla Security Checklist has been considered and double checked (this is not just for security but also for 100% Joomla functionality)
(6) Also ensure that the FTP Layer is installed and working, especially if you do not have a PHPSuExec enabled web server (it's best to use FTP Layers with a massive-long-complex-password account you create anyway, just set-and-forget and never worry about permissions)
(7) Reboot your server if required
(
Reinstall
(9) Ensure incompatible/conflicting extensions such as yComments (and nearly everything those same guys make grr) are disabled everywhere (Plugin AND Component), some may to be UNINSTALLED.
(10) If worse comes to worst, you wwill have to install a new Joomla website (to a subfolder or something) and test JoomlaComment on a brand-new Joomla install, but on your same webhost. If it doesn't work then that means it's a server issue, if it does work then that means there's something in your original server that is broken (or breaking !JoomlaComment).
Long I Know, but this is the sad truth of solution when we cannot reproduce a bug.
Also, I am assuming you have Joomla 1.5.15 and JoomlaComment 4.0 RC1, however may I also ask as to the versions of your PHP and the MySQL (database) on the server? You can find it in Joomla > Help > System Info.