[Solved] I can now see availability of [my-skype] contacts and make skype-to-skype calls because I did:
# mv ~/Skype/[working-skype] ~/.Skype/[my-skype]

Detailed Steps to Fix (all done from n900):

1. find a [working-skype] account to login where you can see contact availability.

2. logout of all skype accounts.

3. Open [X Terminal] and do:
# cp .Skype .Skype.backup
# cd .Skype
# ls
# mv [working-skype] [my-skype]

4. login to [my-skype] and send a [Skype IM]. The n900 will ask which skype account do you want to use for the contact and select [my-skype].

You should now be able to see the contact as online and make skype to skype calls again.

For other contacts repeat step 4.

Note: Keeping the skype [echo123] contact on the desktop will show if skype availability is working.