Btw @aldostools any tips about it?
Before try anything, be sure that the option "Disable content scan on startup" in /setup.ps3 is checked.
Now that said, I only have experienced sync issues starting PS2 games and sometimes when I use an old DS3 controller with the battery almost dying.
It could be a hardware problem, if the sync issue is specific to one controller.
Also try disabling the boot_init.txt, autoexec.bat and the randomizers that execute when webMAN MOD starts.
