So, just wanted to share my conclusions on similar issue with my Melzi. I eventually reinforced the ground plane by soldering an additional cable directly to the ground pin of the heatbed FET and connecting it to the ground terminal on the Melzi power input. This patch eliminated my temperature oscillations. I imagine the root cause for this problem is that my pcb is manufactured with too thin copper layer, as other Melzi users do not seem to have these problems. However, I still have problems with unreliable usb connection, not sure if this is related.
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