SW DOC Manager Issue

I am using a compiled program incorporating the Doc Manager to pull the XML stream of hierarchial data from assembly structures without opening the assemblies into memory. It has works extremly well and is very very fast. However I have run into what I think may be an API bug. I have an assembly which has one sub assembly that is set to Flexible. When the program I created runs against the parent assembly it does capture the top level sub assembly (the one set to flexible) in the output, but none of that subs children or parts are in the output at all. Anyone run into this? I know what Flexible does, but for the life of me I cannot figure out how it messes up assembly data stored in the file.