This happens with 4.0.5 beta as well. If you do a checkin from VS2005, any C# files that are open will have all their #regions expanded. you then have to manually collapse any #regions you wanted to collapse. Any files that are closed at the time of checkin are not affected.
I don't program in VB, so I don't know if it is affected as well.
EDIT: Here is a macro for collapsing/expanding just the #regions in a C#/VB file. This is useful because the built-in functionality of VS (all versions so far) is to collapse all collapsible elements (classes, namespaces, etc...). So these macros help since they collapse/expand just the #region elements: http://blog.wouterdeboer.nl/archive/2006/07/24/17.aspx
Bug report: #region expansion upon checkin (C#, VS2005)
Moderator: SourceGear
Bug report: #region expansion upon checkin (C#, VS2005)
gabriel magana-gonzalez