I have following problem: my eclipse Oxygen fails to run(error attached). Everything is fine on fresh instalation, when I run it just after downloading (tested on 1a september and 2 december). However, when i restart my computer, eclipse won't start again unless i will reinstall it. I have cleared both eclipse cache as same as my project (even fetched fresh version from repo), workspace and eclipse instalation place is also fresh. I have read e.g. https://bugs.eclipse.org/bugs/show_bug.cgi?id=475392, https://bugs.eclipse.org/bugs/show_bug.cgi?id=514895 and other related posts, didn't help though. Any idea? I am working on windows 10 64 bit, and JDK 9.0.1+11. My only plugin is BndTools 3.5, latest, project requires java 8 (current runtime jdk is 152). Problem started on friday, 15 dec after running my project and resolving dependencies at example bnd project (http://enroute.osgi.org/tutorial_base/600-testing.html) at the same time. Couldn't run eclipse after that. However, i did it before and didn't meet any problems (i mean opening example and running it). Also, I have cleared p2, mvn and bnd cache.

Below mentioned stack from eclipse .log:

!SESSION 2017-12-18 16:47:57.660 -----------------------------------------------
eclipse.buildId=4.7.2.M20171123-0800
java.version=9.0.1
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=pl_PL
Framework arguments:  -product org.eclipse.epp.package.java.product
Command-line arguments:  -os win32 -ws win32 -arch x86_64 -product org.eclipse.epp.package.java.product

!ENTRY org.eclipse.osgi 4 0 2017-12-18 16:47:59.711
!MESSAGE Application error
!STACK 1
org.eclipse.swt.SWTException: Invalid thread access
    at org.eclipse.swt.SWT.error(SWT.java:4533)
    at org.eclipse.swt.SWT.error(SWT.java:4448)
    at org.eclipse.swt.SWT.error(SWT.java:4419)
    at org.eclipse.swt.widgets.Display.error(Display.java:1263)
    at org.eclipse.swt.widgets.Display.checkDevice(Display.java:767)
    at org.eclipse.swt.widgets.Display.addListener(Display.java:628)
    at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.<init>(IDEWorkbenchAdvisor.java:187)
    at org.eclipse.ui.internal.ide.application.IDEWorkbenchAdvisor.<init>(IDEWorkbenchAdvisor.java:195)
    at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:152)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:564)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1499)

Diff between fresh and dirty instalation

Update

After flushing whole system, problem gone for a while, however came back again, so it eliminates OS influence in my opinion. As Struarf mentioned in his answer, deletion of configuration/org.eclipse.osgi templorary solves problem. Nevertheless, when i have installed oxygen 2, I noticed that this problem is much more rarer than before (actually now 2nd time for 2 weeks, whether before was with each possible occasion), so maybe it comes in a good way...

I've just commented on bug 477247. I'm getting a similar exception (on OSX). What allows me to start Eclipse without reinstalling is to delete the configuration/org.eclipse.osgi folder. It looked like a bundle cache, and deleting such caches has worked elsewhere for me. Hopefully this might also provide a clue for the devs.