In teamcity MSbuild.exe incremental clean causing issues -

so have 2 projects copies of each other in teamcity. 1 qa , other stage. difference between 2 pull 2 different branches in repo , use 2 different pubxml's. pubxml's supposedly same except publish url.

for publish step use command line build step calls msbuild.exe , uses pubxml publish files. in stage in build log see there incremental clean section several of our dll's being deleted checkout directory. understandably not being copied deployment server. in qa isn't happening, in fact there no incremental clean section @ all. files copied on , no problems.

can explain happening? causes incremental clean step occur during msbuild.exe , how can stop it?