Maybe the problem is that in your .pro file you should have set different target directories or different target file names. I do not know why but it looks like on Windows the target file names generated into your Makefiles are different and on Linux they are not different. You can try to change either your target directory or your target file name for debug build. Try either
CONFIG(release, debug|release) {
TARGET = plugin
} else {
TARGET = plugind
}
or
CONFIG(release, debug|release) {
DESTDIR = release
OBJECTS_DIR = release/.obj
MOC_DIR = release/.moc
RCC_DIR = release/.rcc
UI_DIR = release/.ui
} else {
DESTDIR = debug
OBJECTS_DIR = debug/.obj
MOC_DIR = debug/.moc
RCC_DIR = debug/.rcc
UI_DIR = debug/.ui
}