Tom,
I'm running out of things to suggest, but I'll give you some things to look at, some potential gotchas.
On your flow diagram, is Options at the top set to Multiple files?
Referring to your answer to question 2, is it on every record?
If that's not the same as your Trading Partner ID, I'm guessing you need to define that field in your record structure as a key field. Then on the header level of your flow you would note it as the key field. Every level under the header you would note the child record's field that will be same as the header as the Key field and then for match field would be the field that's on the header record.
If it's the same as your Trading Partner ID, then you just flag the field in the record definition as just that, then use the "+" on the flow properties' key and match fields.
Referring to your answer to question 3, I was trying to get at the general parent/child/sibling structure. If it's a complicated structure, then I would double-check that the levels and their associated segments are logically assigned. That repeating levels are flagged as that; ditto for mandatory segments. Also, anything that belongs to the header is on a level under the header (Parent level would be header level). Anything for detail you would probably have as a child of one of the children of the header or the header itself. For looping levels, Next level would be the same level. For one-time only levels, Next level would be next logical level down except for the summary level when the next logical level is Header level. Additionally, Break level could be a parent level or the next level down depending on what you want the map to do when there are no more records of that type are found, when the I/O rule for that level fails.
I'd like to give you hard and fast rules for flow, but it all depends on the situation and what you want to happen. Early on, many of the problems I had, I had with flow, so I sympathise. I have never had ECMap generate a flow that I didn't have to tinker with except, perhaps, for compliance maps where it had to test everything. I also tinker with levels and flow before I generate the map; adding a new level in later never seemed to work right.
Well, this is a long-winded answer, but it's just that I can't pinpoint what your problem is. If I'm no help, try Sybase; they'll ask you to send them your map, but they're good at diagnosis usually.