I have just experienced the same problem, a bit abruptly I might add since we are trying to invoice and ship castings.
I do not think this logic sequence is failing due to any customization, but rather from the initial loop logic from the default Sales Order to Invoice loop from the Method default screens. Possibly this default screen was fixed and pushed out, but anyone who has built a custom screen from the Method default screen logic will abruptly have their application break.
I think this "logic validation" is a really bad idea and needs to be fixed. It could have a much more graceful error handling, more professional and technically clear without the verbose and chatty message. The logic should be allowed to proceed such that a working application can continue to work, but administrators would receive notification from their users that they are getting error messages every time they create an invoice, or even an e-mail notification.
This logic validation could have been implemented in the background with a log file to provide some visibility to the Method developer about how many production screens would choke on this new rule, before it was rolled out with a hard FAIL implemented in the logic. The redirect to login to the old version of Method is also a clumsily implemented solution. The new login opens a fresh session in a Popup Screen, not a new Tab in Firefox and presents the user with a really awkward session to try to use without a link for future logins, etc.
The logic worked before, as the standard Method screen, and as our customized screen, so this is really a false error. I understand the need to provide more logic validation, but breaking applications turned over to production for purely stylistic or symantic errors that the script handler already knows how to handle gracefully, is really bad software design.
I think I can fix our screens here in a hurry, but we really shouldn't encounter this. I think this is just a little too fast and loose with code change to the Production Version of Method.
Cheers,
James