The problem you're having is with buffering.  There is no guarantee that you will get STDERR results and STDOUT results in the same order each time; in fact, it's quite likely to change from run to run.  Sometimes you might get all of your STDOUT at the bottom, and other times it might be interleaved.

If you really need to capture both STDERR and STDOUT, and especially if you care about the ordering, using "backticks" (` `) may not be the best way to go.  Why don't you give an example of what you want to achieve, and especially some of the code you've tried, and maybe we can help you brainstorm other solutions.