SharePoint 2007 WSP deployment process, restarting SPTimerV3 service

Question

I've got a WF feature which I've been deploying into my development/test environment fairly frequently, and as such have run into an issue where the assembly seems to be cached by the SharePoint Timer service (SPTimerV3), and then an out-of-date version is used after the workflow rehydrates following a Delay Activity.

To fix this, I've tried adding a "NET STOP SPTimerV3" and "NET START SPTimerV3" to my batch file after the STSADM commands to install the .WSP . It works to restart the timer service, and I no longer have the caching problem, however restarting the timer this way seems to kill my SP App Pools in IIS fairly regularly.

Has anyone found a good way to restart the timer in a WSP deployment batch file without adverse affects? Do I need to restart another dependent service, or restart the App Pools each time as well?