Sometimes, when I launch some process who uses mySql a bit drastic (the last is a script to write in core_rewrite_url about 3000 line of new redirect), or when I change theme, Magento is so slow to load pages and doesn't load JS or CSS, with 404 errors. This if I reload frontend or backend in the same browser. If I open it on another browser (not a new window, a different browser, like chrome), everything is working fine. This appends on different PC, but installation is same hosting server. Flush cache, reindex, logout doens't resolve.
After some hours, everything return to works fine.
It could be a Linux server problem? .htaccess? gzip?