The plot thickens... turns out all games are afflicted with 1-second pauses when Eclipse is running. It might just be a daft Eclipse thread doing it.
This is probably due to the idle GC feature in Eclipse. When the IDE detects itself as "idle", it periodically runs System.GC() to reduce perceived memory footprint. This however causes its CPU usage to spike and pauses games and other CPU intensive apps.
It's discussed in this bug: https://bugs.eclipse.org/bugs/show_bug.cgi?id=118335
You can run eclipse with: eclipse -vmargs -Dide.gc=false, as described in the post #8. This disables the idle GC and fixes the pauses, at least for me.
And oh, hi. First post, long time lurker.