This seems to a pure Eclipse problem (no KNIME code is involved at that point in time). A bit of googling shows that it may happen if the workspace is on a network drive. You can try to add "-Dosgi.locking=none" at the bottom of knime.ini.
KNIME starts now but can't save workflows and soem files seem to be locked.
WARN Database Connector 0:429:4 Unable to write to file 'E:\Data\knime-workspace\.metadata\knime\history_database_drivers.txt'
WARN Database Connector 0:429:4 Unable to write to file 'E:\Data\knime-workspace\.metadata\knime\history_database_urls.txt'
FATAL SaveWorkflowRunnable File not found
ERROR WorkflowEditor Could not save workflow: File access problems: E:\Data\knime-workspace\test-workflow\workflow.knime (Access is denied)
I will try to solve issue with sys admin. Seems to be specific to the setup. It works fine when putting the worksapce on the c: drive. (we should put it on other drvie for disk space reasons)