Just wanted to add I managed to resolve this by disabling "Automatic save all files before building" and "Select first warning if built without errors" within the Prefs->Build.
I think the issue is some kind of race condition that results in leksah failing to release the file handles after saving prior to a build. On Linux if you look within /proc/<leksah pid>/fd/ you can see the open file handles and these are the files that you can't save when the bug occurs.
Thanks.