Hello Robert,
I agree with Joseph to check to see if you require prenotes in the checkbook setup, and if so, verify if the skipped vendors have been prenoted or not on their vendor card. (see 'OPTION 1' in the below link to KB 945955 on how to check this.)
Other things to check:
• The country code and bank country/region fields do not match between the vendor and the checkbook. (see 'OPTION 2' in the below link to KB 945955 on how to check this.)
• Another thing to check is to make sure the 'REMIT TO' address ID on the vendor card is the address ID set up for EFT. Check to see what address ID was used on the invoice (VADCDTRO columns in the PM20000 table.)
• If the vendor has some address ID's with EFT banking information and some without, and documents keyed under each, then the check batch should be built first, and then the EFT batch second, in that order. (Read the last bullet point under 'Q21' at the end of KB 945955 in the Q&A section.)
http://support.microsoft.com/help/945955
Hope that helps you more. The KB has all the EFT troubleshooting information in it, so is a good read.
Cheryl Waswick
Microsoft Dynamics GP Support