this happens when you do this
1 windows cd writing is enabled
2 you burn a project of files
3 you leave the disk OPEN(your default settings should be changed to always close the disc)
4 you take out the disc, re-insert it and "1" above opens a NEW session.
5 windows only shows you the LAST(current) session files.
turn OFF windows cd writing, as you have cd writing software
turn on the CLOSE cd option in your cd writing software defaults( this may annoy you for AUDIO cd making where you might want to gradually over a period of days, build up an audio cd )
so what have you got?
you have a disc with TWO sessions(probably the 2nd one is till open.
the disc itself is not yet FINALISED
to SEE the disc data, FINALISE the disc
use a utility like MagicISO, or good cd writing software to view the 1st session data.