It is the way the system operates. Without going into too much detail, when your training staff feels you are ready for the promotion we request the next rating through a separate page in VATUSA. It (the website) then acknowledges the change by temporarily setting your visible rating to that level (i.e. S1). It also shows it in your promotion history which is available to the Instructors and ARTCC staff to name a few (to prevent duplication of efforts). That sends the request to VATUSA, where it is then processed and sent to VATSIM. VATUSA and VATSIM sync their information twice per day (as far as I know) which is normally around 0300z and 1500z if I recall correctty. During this process typically the VATUSA page is reverted back to your original rating, although the promotion is still shown to the above mentioned staff. Once it has been successfully updated at the VATSIM level then it will show again on VATUSA (after the synchronization). You should also receive several emails during this process, from both VATUSA and VATSIM. Your final email with be a notification of rating change from VATSIM, at which time you can expect the rating to be effective within a matter of minutes (typically, although it can take up to an additional 12 hours).
Hope that explains it without confusing you, but as you can see a seemingly simple promotion can take quite a few steps, most of which are thankfully automated.