Well, I don't know what channels on the Portastudio you were using, but here's how the thing works.
The Portastudios utilize each "channel" of the tape cassette as one track. A normal tape cassette gets broken up into L & R sides on each side of the tape. The Portastudio takes this concept, and breaks the tape up into 4 channels based on the L & R of each "side" of the tape. Its why they tell you to only use the tape on side A - if you were to flip it over in the Portastudio and fast forward far enough, you would discover that your tracks are coming through the opposite channel, and they are all playing backwards.
This also means that when you take the tape out of the Portastudio and put it in a regular tape deck, the tape deck is going to play back what was on track 1 through one speaker, track 2 through the other, and you won't hear 3 & 4 because they are now on "Side B" of the tape.
You need to 'mix down' what's coming out of the stereo output of the Portastudio to a separate source, via some sort of stereo output - usually there are Tape-Out RCA jacks for this purpose. It also means you will either need another tape cassette deck to mix your Portastudio's output out to, or some other recorder (be it a writeable standalone CD burner or the line-input of your computer).
