A couple of questions ...
1. What is the Sub-ledger type on the Flex Accounting Rule? Is it consistent with the Location field you are using? (Character , Numeric, A/B validated??)
2. The Location wouldn't be blank for the Inventory transaction you are performing would it????
The Flex Accounting in Distribution has always been a mine-field where certain transactions or certain AAI's don't always work properly (especially with Subledger population).
If no luck your alernatives may be to ...
a. Search for SAR's
b. Try and use another field (eg Reference) as your source field for populating s/ledger
Hope this helps.