Which OS and LR version are you using?
Are the files on a local disc?
LR 6 on Windows 7 Professional 64bit
The files are all on local disks, partly on the same SSD as the operating system, partly on a different disk.
I have the same issue (LR CC2015 under Windows 7).
I'll select a group of images in the Library grid and hit Ctrl-S to write metadata to files. The progress bar suggests metadata is being written, but for some of the images the down-arrow indicating the metadata needs to be written does not disappear. Doesn't seem to matter which of my internal hard drives the files are on, nor whether I select just a few or a thousand files to update.
If I select a single image and click the down-arrow then that usually writes the metadata and the arrow disappears. I say "usually" because sometimes LR appears to write the metadata but the arrow remains. I can't detect a pattern to this behavior.
Using ideas I got from answers in a different post, I managed to get rid of the warnings LR issues, simply by changing the setting "Automatically write metadata changes to disk". Once LR had written everything, the warnings did not pop up again, also not after unticking that option again.