burn arduino bootloader and compiled sketch at same time
If you program via ISP, it erases the boot loader, because you do not need it. The whole point of the boot loader is to allow programming over USB. So if you want to use the normal Arduino USB input to program, burn the bootloader and then do not use the ISP.

Note my knowledge of this dates back to older arduino ~1.0 software, it is possible modifications have been made, but the above should still be true. If you have an ISP you do not need the bootloader at all.