This is the actual problem that cause trouble. Your flash drive is probably Fat32 or NTFS formatted rather than ext4. Since those file systems do not support "executable attribute", Linux will silently fail to give files the attribute which results in these sort of surprises. You may wonder why the same thing doesn't happen on NTFS formatted partition of your hard drive. I guess this is because Linux assumes internal hard drive is trustable, thus all files have executable attribute by default (that's what happens on my pc).
Just wanted to thank everybody again and do a recap. Yes, it was the FAT32 flash drive. I read that FAT23 supported rw on both Windows and Linux but was ignorant about the "exec attr". Redid everything on the flash drive formatted to ext4 and everything works fine between both systems. (need to install Ext2Fsd.exe on Windows, however).
