I think I figured out what happened on this by looking at the sales spreadsheet downloaded from ebay's file exchange and crossing it with MCP. What I noticed is that for transactions where buyer orders more than one item in a single transaction - there is an "order id" and under that order id each item has it's item number-transaction number. But when imported into MCP, the order id is pulled and picked up in scientific notation.
Also, I noticed that for some reason i had one item where on ebay's file exchange the transaction id was in scientific notation so that is the item I mentioned was missing from MCP that I added manually and it later was overridden when I downloaded more sales. I figured that part out too...if you create manual entries you have to add the item number-transaction id which is a unique value -- i had that field hidden so I forgot to enter it (plus you don't see it unless you are looking at a file exchange document)...but once I figured that out and added it back, the entry now sticks.
So some of this problem is probably bad info coming from ebay - I'm overwhelmingly impressed with this spreadsheet - just trying to figure it all out
Thanks again - I just wanted to update you with my findings.