Zencart V1.3.8a with QBI 3.2.1

Have a few issues and I'm not sure if they're setup problems or bugs:

1. Only a fraction of my orders are importing. When I look at the iif file, it goes from 976 to 1325 for no apparent reason. In QBI, here is what I see:

All Previous Orders
Quan: 68
No.: 901 to 1554
Date: Dec 8, 2009 5:39 pm to Nov 9, 2010 1:38 pm

2. I have Matched every shipping method and I still see "Ship Via" in the iif file says "Method not set". It looks like these orders are the ones that are "Free shipping" but I have that matched to
"USPS Priority". The option "Method not set" doesn't even exist in the matched list.

3. Paypal Payment method is coming across as "Check / MO". I've checked this and double checked it. Under payment setup, I've set "Paypal" to "Paid online" and under match I've set "Purchase (paypal)" to "Paypal". Under configure I have "Invoice terms paid online:" set to "Credit Card" and "Invoice terms not prepaid:" set to "Check / MO"

So it looks like I'm missing something but where?

Thanks in advance!