> Does anyone have had the same kind of problems and is there a solution?

I do have the same problem on Linux with latest Lazarus SVN. 

Behavior of Running/Compiling/Building is not quite well performed (I have on 
mantis an open issue regading the problem with suggested changes which is 
still open about year). 

Anyway, this is not related to synapse, it seems there is some conflict with 
debbuger and some system pasckages/libraries. 

Only solution is what you already found - to build project and run the 
executable out of Lazarus.

Sasa
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www.szutils.net

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