Stuart,
I hear you. I'll start off by giving a little background into the mechanics that go on behind the scenes:
1. When there is even the slighted bit of corruption in any of the lists or transations in QuickBooks, it tends to not be forgiving to apps that add on to it. Since Method integrates with every list and every transaction in QuickBooks, Method is especially senstive to this.
2. When Method integrates with QuickBooks it opens a connection to QuickBooks, processes events, and then closes the connection. If, however, QuickBooks has corruption, it tends to crash the connection, and doesn't let apps like Method gracefully close the connection.
3. When you try to close QuickBooks, change companies, or perform a backup, it will stop you if it thinks Method is connected to it.
4. Method actually creates a "subscription" to QuickBooks that pretty much says "when you open up a company file, can you please open me up too?".
5. As soon as Method opens, it begins a sync with QuickBooks, and opens the connection back up again with QuickBooks while it is doing the sync.
So, that's a little background - most of which you likely already knew, but useful knowing anyway. The reason Method kept opening up is that QuickBooks kept closing and reopening your company file, and then QuickBooks opened up Method because that is what Method had asked it to do. There is no way for us to say "open up Method when you open the company file, but only in situations where you are not doing a verify and rebuild data". So it's all or nothing. I think this is a necessary evil where the benefits outweight the drawbacks - otherwise you would always have to remember to manually open Method each time you opened QuickBooks.
The only reason this became tedious in this scenario is because your QB file had some corruption, causing you to have to do a verify and rebuild. In all normal day-to-day usage, it wouldn't be an issue at all.
Sounds like everything is working as it should. Perhaps the best solution to prevent it from being a paid in this scenario would be to have some kind of option when Method opened that said "starting sync in 10, 9, 8.......1" where you could click Cancel. That way it wouldn't open a connection to QB and you wouldn't have had to shut it down.
Hopefully that makes sense, and doesn't leave you more confused than when you started!!!
Have a good weekend,
Paul