Just having a discussion with a colleague , she made some changes in configuration and now when she creates a simple (not a system) stored procedure in master database it saves under Programmability --Stored Procedures--System Stored Procedures. Is it comfortable? No,right? After some investigation I found that we need to return 'allow updates' to 0 , see below script
EXEC sp_configure 'allow updates',0
Now everything got back to work in the 'right' place.