That message to my knowledge is produced while the make (aktually the internal make) is checking the *.d (dependendy) files you will find in our output (debug) folder. The dependency files are produced as part of the (previous) build.
a) Make a clean (or remove the Debug folder) to see if it makes a difference
b) checke that the refresh policy is using the correct settings (Eclipse Project ‘Refresh Policy’: Broken Incremental Build with External Make? | MCU on Eclipse )
c) make sure you are not using a low latency file system (e.g. a network folder) for your project/files
d) make sure that all your files are local (no far remote linked files/etc)
e) keep the path to the project as short as possible (check the file/file length in the *.d files to get your current length)
I hope this helps,
Erich