Ah! I think I see where the problem might be. I open two files, one in Dropbox, the other in OneDrive for Business. This is what I get:
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(…) returned error code 5.
22:38:27.062 [AWT-EventQueue-0] INFO net.sf.jabref.logic.importer.OpenDatabase - Opening: C:\Users\xxx\Dropbox\xxx\litnotes Dropbox.bib
22:38:27.668 [AWT-EventQueue-0] INFO net.sf.jabref.logic.importer.OpenDatabase - Opening: C:\Users\xxx\xxx\Litnotes OneNote.bib
22:38:29.245 [AWT-EventQueue-0] ERROR net.sf.jabref.FallbackExceptionHandler - Uncaught exception Occurred in Thread[AWT-EventQueue-0,6,main]
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.substring(Unknown Source) ~[?:1.8.0_121]
at net.sf.jabref.gui.JabRefFrame.updateAllTabTitles(JabRefFrame.java:1664) ~[JabRef-3.8.2.jar:?]
at net.sf.jabref.gui.JabRefFrame.addTab(JabRefFrame.java:1682) ~[JabRef-3.8.2.jar:?]
at net.sf.jabref.gui.JabRefFrame.addTab(JabRefFrame.java:1704) ~[JabRef-3.8.2.jar:?]
at net.sf.jabref.gui.JabRefFrame.addParserResult(JabRefFrame.java:1395) ~[JabRef-3.8.2.jar:?]
at net.sf.jabref.JabRefGUI.openWindow(JabRefGUI.java:134) ~[JabRef-3.8.2.jar:?]
at net.sf.jabref.JabRefGUI.(JabRefGUI.java:63) ~[JabRef-3.8.2.jar:?]
at net.sf.jabref.JabRefMain.lambda$start$1(JabRefMain.java:128) ~[JabRef-3.8.2.jar:?]
at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:1.8.0_121]
at java.awt.EventQueue.access$500(Unknown Source) ~[?:1.8.0_121]
at java.awt.EventQueue$3.run(Unknown Source) ~[?:1.8.0_121]
at java.awt.EventQueue$3.run(Unknown Source) ~[?:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_121]
at java.awt.EventDispatchThread.run(Unknown Source) [?:1.8.0_121]