After searching these forums for a multitude of different search criteria I discovered that the issue with LEI and how it sends empty fields from Notes. I'm surprised this wasn't happening all along.
I'm looking to upgrade my Domino server to 6.5.6 to allow the use of the NOTES.INI parameter of EIOracleMapEmptyToNULL.
If anyone knows another way around this within LEI let me know. I can't be making design changes across 20 databases to accomodate this.