Import DB schema not syching well-Display changes

[kepNCI]

Several weeks ago I created new data models for 5 SQL 2008 databases via Import DB Schema from ODBC.  All went well, except I do not like the display it automatically creates.

I changed all of the connections to direct and repositioned the objects to enable easier viewing of relationship and even pinned the end points of the connection (something I typically do not do)

Today I tried to obtain any updates be re importing.  This has work many time in the past for me with the same EA build, however in these cases, EA is changing all of the connections back to custom and re-arranging all the objects, this messing up all the work I did it re-arranging the display.  It did keep by end points pinned.

Any clues on why this is happening?
The only differences between these imports and others I have done is that in these cases I am importing Stored Procedure, User Functions and User Sequences whereas I typically only import the tables and views.  

Here are details:
Using EA 1010.
Settings on the Import DB Schema from ODBC source window:
Options:
  Schema/Owner:  blank   (will except all that are found)
  Include System Objects: No
  Include User Packages (Oracle): No
  Include User Views: Yes
  Include Length Semantics (Oracle): Yes
  Include Triggers: Yes
  Include Default Constraints (SQL Server): Yes
  Include User Stored Procedures: Yes   Import as class operations  
  Include User Function: Yes   Import as class operations
  Include User Sequences: Yes   Import as class operations
Synchronization:
  Overwrite Table/Column Comments: No
  Overwrite Column Default Values: Yes
  Overwrite Check Constraints: Yes
  Import as New objects: No
Import To:
  Diagram and Package