Sometimes there may be some confusion between the global check ins off the dashboard vs work order check-ins vs the time entered on the work order and timesheet.
The global check ins (which are reported in the 'user check in' report) are simply the result of the employee checking in and out for the day, not related to any work order or timesheet entry. These values will not be automatically reflected in the timesheet but are just to indicate when the employee started and ended during the day.
The work order check-ins are when a user checks in and out at a jobsite. When they check out, the user has the option to add time to the timesheet as a convenience. The time is calculated from the last check in to the current check out. If they choose to enter the time, that time will appear in the 'Time and Materials' section of the work order and will appear on their timesheet. These values could be adjusted after check out by editing them on the time and materials settings.
There is also the ability for a user to simply add time into their work order (or timesheet) without a check in/out. If they do so, there will be hours reflected towards the work order and in the timesheet that do not have a reflecting check in/out.
Reports
The 'User Checkin Report' reports on check in/out on the dashboard (so the global check in/outs). The report calculates the time in between a check in/out however these hours are not automatically in the timesheet.
The 'Work Order Check In/Out report shows the check in/out entries for work orders. The data on this report may be reflected on the timesheet only if the user chooses to enter time into the work order on check out, if they choose not to, then the time in between check in/out will not automatically appear on the timesheet.
SUMMARY
The data in the user check in report is really unrelated to the data on the timesheet, as the user check in report shows the check in/outs for the period with a calculated value for the hours in between.
The work order check in/out functionality only adds time to the timesheet if the user chooses to enter time at check out, but the time could then be adjusted afterwards by editing the entry.
The timesheet shows an itemized view of the time spent in the day, either on a work order or timesheet items like 'vacation' or 'Shop time' or whatever other timesheet items have been set up in settings.