Eugene
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Too much overshoot? Increase D, decrease P.
Response too damped? Increase P
Steady state error (like you are seeing)? Try increasing the I constant.
The values I have on the latest version of Marlin have been working well for me with the printers at our office. You can find it them at http://docs.trinitylabs.com. (I'm on my phone or I'd cut and paste them here..)
As a personal preference, I remove almost all temperature control from Slic3r. Other than having it turn off the heaters at the end of a print I don't have it set any temperatures at all. I don't find it inconvenient to set the bed temperature in pronterface and I like the flexibility of being able to start a print when I want to and change the temperature without being overridden at the start of a print.
-Eric
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tl;dr: tune your values to how you want them, then enter M500.If you change it in Configuration.h and power your printer on, you should notice no change - the change only happens after "reverting to factory defaults" (via M502) but again, these would be lost on printer restart unless you save with M500.After tuning the values, enter M500 as you did before, which takes your running config and saves it as your startup config.If you modify the Configuration.h, this will only change your "factory default config", not your saved config or running config.Disclaimer: I have never tuned my PID, but this is based on other values stored in EEPROM and this will most likely apply to your problem...When you power your printer on, it loads the "saved config" into the "running config", which is why you are losing the setting when you reset.
After changing it via the M303, this is saved in your running config.