I've been working on a new R pi 3B+ for the last month or so. I'm running Raspbian stretch. I've added an Adafruit ultimate GPS. I'm supplying power via the 5 V pin. I'm running headless and use VNC or putty from a Windows 10 laptop. I have an RTL SDR connected to a USB port.
This morning while debugging my java application I started receiving an error message after typing "java -jar filename.jar", the message is "unable to access jarfile filename.jar". After a few Pi reboots and repowers nothing changed. I even rebooted the laptop. I even tried to run an old HelloWord.jar file and got the same error. Next was to reimage the SD card to an image done 3 days ago. I received the same error with the HelloWord.jar. At some point later I noticed ntp wasn't working properly. It was receiving GPS time but was not sync'ing to the PPS signal nor sync'ing to GPS messages. Both of these (java & ntp) seemingly unrelated programs stopped working around the same time. Next, I got a second SD card and loaded the same 3 day old image on to it. This resulted in the same behavior where I could not run java and ntp wasn't syncing. I then went out an purchased a brand new Pi 3B+, attached the Ultimate GPS and power, placed the 1st SD card in the slot, powered up and this new Pi behaves identically to the 1st Pi. Both ntp and java are not working. I powered off the 2nd Pi, put the 2nd SD card into the 1st Pi, did NOT connect the Ultimate GPS, applied power via USB, and got the same error when trying to run java.
I'm left with nothing else to try and looking for any help that can solve this dilemma.