an short update:
uploading has no problem --- tried to upload a 26M .wmv video, took 22 minutes, and succeeded. the problem is conversion -- when converting .wmv to .flv, 30 seconds video became 17 seconds. the php package is phpfox.
when upload a .flv file which no need conversion, no problem at all.
php 5.3.26, directadmin, lsws 4.2.3