Okay, there were a few comments on both Amistore and IndieGo! Appstore blog entries that may clear up some issues I had at the time (I plan to revisit each when they are out of beta).

For AmiStore, I had an issue with being redirected to PayPal and my system defaulted to using NetSurf 3.2. This version of NetSurf 3.2 had limited javascript support and Paypal was complaining about it.

Two solutions were suggested:

1) Change the default URL handler in the system prefs to use another browser, such as OWB
2) Completely disable javascript in Netsurf and Paypal would fall back to a non-JS method of processing the payment.

For IndieGo! I had a few concerns and the author of the program left suggestions for each:

1) When selecting the platform, I could only scroll using the arrow keys. Apparently, if the mouse pointer is over the list, the wheel should work. He said selecting more than a single platform selection will be supported in the future.

2) The download speed after purchasing an item was unbelievably slow. This turned out to be a buffer size setting that he said was easy to fix:

Open with a thext editor the file
Edit the line nr. 10:
[SIN]dlchunksize =
And replace the 64(Kb) of buffer with a higher value like 128 or 256 to speedup the download

Full re-review when final versions come out.