Once you start hand editing a form you shouldn't be re-entering the wizard. It sounds like most of your problems are after modification or after several modifications. The key would be to figure out what else changed between those modifications to figure out the cause of the problem.
If you have a form that breaks once you modify it that we can use for testing to reproduce the error then we could run it through some tests to figure out the root cause and try to address it.
I'm not really sure what you mean by "size of text fields"... do you mean the width specfied in the css? It would be very odd to see this happen without changing the design. The design determines the css settings.... do you have a sample page where you have had that problem.
The complicated DIV structure of the forms is necessary to facilitate the miriad of options we expose for styling the form. It is the most flexable html structure we could come up with, but certainly not the simplest... more like the most complex you would ever need.
Several people have suggested that we offer an "unstyled" form version. It would probably have to disable all of the design settings since they depend on the div structure to work, but this will be a likely addition to a future version.
The key for us to be able to solve a bug is reproduction. If we have the necessary files and steps to reproduce a problem, we will do it and fix the problem. I'm afraid the limited details you provide are still not enough for us to definitively come up with a cause.
I can have someone from QA try editing multiple times, but it would help to find out what your original settings were, since that could have had something to do with it. Really a specific file or steps are the best thing to provide for us to be able to work on a particular issue.
You say the extensions are useless because of form builder... did you know that form builder isn't necessary for any of the other extensions to work. It is in fact one of our newest extensions and all of the others worked before form builder ever existed. You can always create forms by hand and use the rest of our extensions on those forms.