My HELOC and reco[n]ciliation

I'm not exactly grasping what the problem is here because you haven't provided any detail about the "weird booking" that has occurred.

The general recommendation when setting up a HELOC is to make it a "manual" loan - a loan where you make accounting entries as transactions occur - and that operates very much like a credit card.  That is, like a credit card, money flows in - you make payments - and money flows out - you draw on the loan to make various purchases.  Because money flows in and out and because a HELOC doesn't have a fixed amortization schedule, you wouldn't create the HELOC Account as a regular Loan Account. 

So if the bank draws money from the HELOC - maybe for fees or something - you simply make the appropriate accounting entry in the loan's register. 

Debit (increase) Loan Fees Category     $XX.XX
Credit (increase) HELOC Account          $XX.XX

Have you perhaps set this up the HELOC Account as a "downloading" loan of some sort, an Account where you have no access to the loan's register in Quicken and only bank loads affect the Account?