I have an open case with Marketo support about this, but I wanted to see if anyone is having the same issue. We have custom fields that are being updated through form submissions on the Marketo side, values are being added to the contact fields in Marketo, but they are not syncing over to Salesforce. When I spoke to support, we did a test by updating the fields on the Salesforce side with different values and it pushed over to Marketo, then we updated in Marketo to what the values should be and it pushed over to Salesforce fine. Marketo support said this is common across its customers, but I'm having trouble understanding the route cause of this issue so it can potentially be avoided in the future.
Do you see any SFDC sync error from earlier when you were experiencing the sync issue? Also, did you experience sync issues only for updates to the contact records via form-fill?
If I understand it correctly, custom fields updated via form-fills for the contact records aren't not getting synced over to the SFDC (although data seem to sync properly when updated manually on either side), this is really strange, and on top of that there aren't any sync failure notification/activity logged in Marketo! FWIW, this issue isn't v. common (at least to me).