Every month when I download transactions via Web Connect one or two or more are skipped

QuickBooks imports bank transactions in a file format called OFX.  Each transaction in an OFX file has a unique transaction id.  Below is an example - in this case the transaction ID is the number following <FITID> or [removed].   The numbers _must_ be unique - they can never be used in the same bank account for two different transactions.  If they are that's a bank error (Collect $200! No, just kidding!)

QuickBooks keeps track of the transaction ids that have been imported and what you've done with them. For instance if you delete a transaction from the download transaction window QB will track that FITID number.  Next time you pull transactions from the bank that same transaction may get pulled down again.  If it is, QB will see that you already marked it "deleted" and it won't show up in the list of downloaded transactions. 

<STMTTRN>
<TRNTYPE>CHECK
<DTPOSTED>[removed]00[0:GMT]
<TRNAMT>-2853.00
<FITID>[removed]
<CHECKNUM>3070
<NAME>CHECK 3070
</STMTTRN>

So, since you are using WebConnect, you have the .qbo file.  Open that in text editor and find the transaction that isn't being imported.  You can change the FITID for that transaction to something different (make it wildly different - like add 7777 to the end of it) and try importing the qbo file again.  If the transaction now comes in the issue is the original transaction id. 

The question then is whether you've already added that transaction to the register or if you've marked it for deletion.  In either of those cases QB is working as designed.  It has to do this to prevent duplicate entries and ignoring your commands to delete a transaction. 

The more insidious case is if the bank isn't marking the transactions uniquely.  In order to determine that you have to search all your .qbo files and see if that transaction id has been used previously in one of them.  Spotlight can search them so just typing the transaction id in Spotlight may tell you - if you've kept all your old .qbo files and haven't deleted them.  

If the vegetable is rutabaga that's your problem. QuickBooks hates rutabaga. 

Seriously its difficult to determine the cause of a dup FITID unless you happen to have a smoking gun showing it used twice.  But you can proceed with the fix you have. Keep your old .qbo files in a folder in case it happens again.