I have separate accounts in two different countries both of which I have residence and bank accounts - when I change from one account to the other on my iphone then I get a message that says that for 90 days I cannot access the other - any ideas?

That sounds like the "90 day switch" rule related to changing Apple IDs. Whenever you enable automatic downloads, turn on iTunes Match or download previous purchases your device or computer becomes "associated" with the ID currently in use. Once associated in this way you cannot change to another ID for a period of 90 days (read more here: http://support.apple.com/kb/HT4627). I suspect this rule was necessary to prevent piracy as it prevents one from quickly signing into a number of their friend's IDs and download their purchased content.

This is correct. These are the terms and conditions for using the iTunes store, so there is no way of changing this behavior.