VC3.1 300 - Chaos on the Y Axis

Hi there,

Have been putting my VC3.1 back together after moving house but I am seeing chaos on the Y-Axis input shaper graphs.
It's running RatOS 2.1, the stock motors with 4 Beam Ruland Decouplers, BRS Belt Tensioning M2 in PC-CF, Toro-Tube & Toro-Rail, Honeybadger medium-preload Y-Rails, and new bearings on all points.

After putting all the parts back where they belonged I cleaned my X & Y Rails with IPA and re-greased with EP1. All running smooth with no weird issues felt.
Re-aligned the Y and X-Rails to make sure they are parallel according to the commisioning guide.
Then went through the belt tensioning process which seems to be good enough for now.

At input shaping I'm seeing a clean-ish X-Graph but absolute chaos on my Y-Graph and I have no idea what to look for. Tried to see if anything was rattling using the resonance tester but nothing I could find.
See attached the results of where I am at now.

Any ideas what might be causing this?
belt-tension-resonances-2024-08-28-100511.png
resonances_y_2024-08-28-101311.png
resonances_x_2024-08-28-101006.png
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