Hello,
well if the SlideShowPro does modify the .htaccess in the Joomla root directory, then it is quite obvious that JoomSEF will not work and you will get 404 messages, as the added directives disable the SEO. Specifically the code:
# <IfModule mod_rewrite.c>
# RewriteEngine Off
# </IfModule>
If the SlideShowPro works even when these are commented out, then it is fine and I believe you can run both.
If not, then some special set of rules might be needed to make sure both SlideShowPro and JoomSEF will run. That would however already be out of range of these support forums - anyway we could still solve within a paid Joomla support we offer