Your latency -what is it, what are your inputs/outputs, how are you measuring it, what presets are you using, etc, etc.
Pretty much all digital systems with analog i/o have a delay between input and output, beyond that provided by processing. This is due to the length of the filters in the A/D and D/A processing, and can be in the order of 1mS. Using digital i/o will reduce this to a few samples.
User presets should always be backed up before a upgrade, especially in this case. If you revert to 3.51 you may find that your presets are accessible – save them to a card and then repeat the upgrade.