If you have a cin >> something; call prior to your system() call.
For example, taking input into an integer.  When cin >> myintvar; (or similar) then the integer is placed in myintvar and the '\n' gets sent along in the stream.  The getline picks the \n up as indicative of the end of a line of input, so it is effectively "skipped".
Either change the cin >> to a getline() 
or call cin.ignore() to grab the '\n'(or better, call a cin.ignore (std::numeric_limits<std::streamsize>::max(), '\n' ); to flush the input buffer-- but be sure you're not throwing away valuable input in the process).