I had this issue before when updating, I ended up deleting the folder and redownloading it and then setting the settings again, for some reasons if you update it or paste it over the top it doesn't auto start any more.
Its not to hard to update depending on how may values are used by HWInfo, for example it took me 30min to update mine, but it can no longer capture max temp readings.
Sorry but I do find the limitation stupid for the free version, people that use your tool for rain meter for instance use shared memory support, limiting the amount of sensors seems more logical to me than forcing it to disable after 12 hours, then again if its using OS time ill just hex edit it.