Solution and Project in same folder causes problem

Working with SourceControl for _all_ systems better to have tree
organized project architecture as shown on this page:
http://www.pushok.com/help/cvsscc/index.php?redirect=basic_addtoscc.htm
This is help to have less problems with initial binding or project
adding.
However, under some circumstances you may have other solution
organization. In such case at least better to perform initial adding
from IDE. If you add codes using other CVSGUI you should fall into
"Binding procedure".
It works strange even for us :).
1. It's logic fully controlled by IDE and we cannot change nothing in
it.
2. When you adding project (solution) IDE perform this in some
"optimal" for IDE sequence (i.e. solution, normal projects, web
projects). When you bind, you are free to change this binding
sequence. That's why probably you have different records in solution
file after bind and add operations.
We do not have trivial advices how to do binding right (again better
to add from IDE initially), but:
1. Manual modification of solution or project files adding "good"
binding is not bad. Files are plain text files, and you will not
damage them.
2. Try to change sequence of binding. I.e. not select all, but first
bind solution, then all projects (or project by project).