Not a question but rather a discovery which may be of use to some others out there. I realize there are newer versions of all the mentioned systems but for a number of reasons the client is required to utilize these.
So on to the problems:
1. All Feature Types (SDE layers) are created in SDE prior to running FME so Writers are created using Import Feature Types rather than using FME to create the layers. Again this is required as part of the business process.
In order for FME to recognize these tables as spatial they must be opened in ArcCatalog/ArcMap first to initialize them without doing this FME tries to insert a NULL/nil geometry and fails.
2. For one particular non-spatial Feature Type, FME kept indicating that there was a missing column although did not specify which one. Google searches indicated it was likely an underlying issue with the SDE table.
To try and determine the issue, we dropped and recreated the table, removed any contraints, keys etc but still no luck. We then created a table with the same schema but a different name and oila...so it appears that there was a metadata corruption in SDE and we had to clean out any references to it.
Hopefully this can save someone else some time as we spent a long time on it.