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I found quite a simple solution to my problem:

Do not maximize the TeXnixCenter-Window but resize it to fit the full screen instead. Now align the toolbars to your needs and close TeXnicCenter. After restart of the program, toolbars should have stayed in place. Now you can maximize the ...

Same problem here. I have experienced the behaviour described by delycs when working quite some time with a previous version of TeXnicCenter. I am now beginning to work on a new long document using the current version. This time I see ONE of the toolbars misalign EVERYTIME I start the program. Any ...