I expect that the DLL has its own instance of the logger, therefore configuring it in the executable doesn't help it. I just had a look at the respective code, but it seems that changing it so that you may use the instance form the DLL instead is not an easy task, as it is quite fragmented. I suggest writing a wrapper-method for OFLog::configureFromCommandLine(...) that your DLL exports, so that it may be called from the application effectively configuring the logger inside the DLL, but still via the command line parameters given to the application.
EDIT: I just had another idea: did you try to build DCMTK as a set of DLLs? Maybe, if the logger is inside its own DLL, it will always have its own instance inside that DLL, no matter where it is initialized from.