loading ecb-mode from desktop.el messes .emacs

[Micha Feigin]

When ecb is activated through desktop.el (an active desktop session was
closed with ecb-active), when next opening emacs it will remove
custom-set-variables and custom-set-faces from my .emacs and inhibit
some of the settings from loading (for example tabbar doesn't load
automatically in this settings).

Any ideas on what the problem is or how to solve or find it?

This is with emacs bidi (based on 21.3.50). desktop.el has something
about version 20.3 and ecb is version 2.21.