Your explanantion doesn't correspond to the circuit diagram, which shows a common ground of IR2210 logic side and DC bus. Actually, IR2110 would never work with a floating ground. You have been quoting the respective IRF applications notes, and this point should be clear from carefully reading them.
I initially understood your motivation for not using the IR2210 low side driver in the expected high noise level. I wonder however, if this is a well-founded decision. The low side driver allows some ground potential differences between logic (VSS) and output (COM) side. Clearly, Vcc must not swing below Vss. But this also not permitted for VB. Just look at Figure 10. IR2110 Parasitic Diode Structure in DT97-3. Floating ground is not permitted, because a return path for the control current between input logic and high side must exist.
My assumption is, that using the IR2110 low side driver for the low side switches involves similar restrictions as using high side only. As I already mentioned, VSS must be connected in any case. I'm not sure, if it's necessary to supply the unused low side drivers (you could use a single high side driver chip in this case as well), but it shouldn't do any harm.
As I also stated, I don't see an indication for driver related problems at present (except for missing VSS connection). It may be the case, that overlapping gate drives are causing shoot-through, or that an unsuitable gate signal wiring results in ringing gate voltages and respective oscillations. But even in this case, you shouldn't get output voltages swinging widely out of the DC bus range. This is either a problem of bad power circuit layout or incorrect probing.