I think that the price for "Intellect" is just mis-numbered; most of the software prices seem to be completely inconsistent with regards to scaling. Which just makes it that much harder to estimate.
But if I had to hazard a guess, you'll note the "Intellect 10" version found in the Ship's Software is 1 million credits; if you were to buy only 1/10 of that, it would be "Intellect 1, TL11" for 100000 credits. I'd put the prices for successive generations at 125% or so; much higher than that, and by the time you get to "Intellect 10, TL20", it would cost 1 million credits again 9 TLs after the ship version. And there being any practical difference between ship software and any other software is just plain ridiculous, when any modern smartphone can do in-system astrogation.
Alternately, if TL11 is "too soon" for you for this sort of hand computer software, there might be a cost break modifier somewhere that offsets the higher TL penalty... but I haven't noticed one, to-date.
Of course, both these options still make Agent programs comparatively too expensive. I think the whole shebang needs to be rewritten.
GURPS has something to say about the cost of the generalized version of something vs. the specialized version, and increased TL requirements to boot. I'd start there when re-pricing the software, using 100000 credits at TL11 as a base number.