Not sure if this will help (did for me, though). Check for and get rid of orphaned files. I use Dave Buckner's TRT File Monitor. Once I cleaned those files out, I had fewer timeouts occurring.
After deleting orphans, be sure to synch database & system files, from within the portal and/or host file manager. You may also have to increase the timeout value in your web.config, especially when you have large portals (lots of files).
Others (more experienced) may have more suggestions, but the above has made a big difference in my DNN installations. Good luck.