I am having a similar problem.  Was hoping someone had found an answer for you.

In my case, there are about 12 total employees. I noticed the TB did not match the Payroll Summary.  I looked at the various PR withholdings and saw that for four of the employees, nothing was showing up in April (seasonal business so this the first paychecks for the year for these particular employees.) 

Just tried to reconcile the bank account and the paychecks cleared the bank, but they do not show up in the register.  Bank account is the same for all employees but only these particular employee checks are not showing. 

Were you able to figure it out?

Thanks if you are able to give me some ideas!