Hi AndrewStephen
I believe the symptoms you describe are actually caused by 'duplicate' records in the price matrix. I have seen dozens of files that have duplicate entries for the same item and same break quantity and price level. One client's file had over 30k - they import price updates and clearly things have gone wrong numerous times - a bug allows the creation of more than one record for an item, for a given price level and quantity. So now when you import (or even update manually sometimes), the screen displays not the data you entered/imported, however it is displaying prices that are in the matrix, just not the prices you want - MYOB seems to update one of the records when you import, but sometimes displays the other). The real question is when invoices are being process and the price matrix has 2 matching entries, which one does it use? Have you ever notices customer invoices with the wrong price level?
To check if this is the cause in your file, get hold of a program called File Utility MYOX, select your file then choose Tools > Check for Duplicates - this runs a dozen or so tests to pick up known duplicate scenarios in MYOX files - most cause Data Invalid errors, but not all. Duplicates in the price matrix don't cause any error messages, just wrong pricing. NB the file must be local so if your file is online, you will need to make a backup and restore locally using a different file name to ensure it does get used inadvertently. Delete the local copy when done checking.
If you find duplicates, no doubt MYOB has a script to fix this too. Obviously better if they had a coding solution that prevented it from happening.
Regards
Gavin