Failure to get a bibliography because instant formatting icon is inactivated after inserting each reference. In the bibliography RM makes for each reference it starts all over again with number 1.
You probably checked this already - but in your Generate Bibliography settings do you have Number Bibliography checked, by Citation Order, and that your output style has in-text citations formatted correctly? If you make an output style without anything specified for in-text, and then use it to generate, RefMan numbers them all as #1.