We encountered same kind of problem with our environment recently, as to why is not yet entirely clear.
However the symptoms were the same, PDF annotation plugin could not find stamp image files and gave
Default exception handler: Can not read file, either file does not exist or there are permission problems
Debug: [dataroot]/filedir/a4/f1/a4f146f120e7e00d21291b924e26aaabe9f4297a\nError code: storedfilecannotread\n* line 454 of /lib/filestorage/stored_file.php: file_exception thrown\n* line 2134 of /lib/filelib.php: call to stored_file->readfile()\n* line 2504 of /lib/filelib.php: call to readfile_accel()\n* line 75 of /mod/assign/feedback/editpdf/lib.php: call to send_stored_file()\n* line 4684 of /lib/filelib.php: call to assignfeedback_editpdf_pluginfile()\n* line 37 of /pluginfile.php: call to file_pluginfile()
As we were in a hurry to get this feature to work we investigated for a while and found no coherent reason. We got pdf annotation working again by first uninstalling Annotate PDF - plugin and then reinstalling it from moodle-2.8 installation package as suggested in the tracker (https://tracker.moodle.org/browse/MDLSITE-2622) so at least that solution works.
Best Regards
Juha Martikainen