System Configuration : Preferences : Operation Preferences : Misc (Miscellaneous) Section

Misc (Miscellaneous) Section
Clip Auto Fade In/Out Length (Pro Tools HD and Complete Production Toolkit Only)
Sets a default length for fade-ins and fade-outs automatically applied to clip boundaries. Using automatic fade-ins and fade-outs saves you the trouble of editing to zero-crossings or creating numerous rendered fades in order to eliminate clicks or pops in playback. Autofades are not written to disk. Value range is from 0–10 ms for the Auto Clip Fade In/Out Length setting. A value of zero means that no auto-fading will occur. The Auto Fade value is saved with the session, and is automatically applied to all free-standing clip boundaries until you change it.
Calibration Reference Level (Avid HDX, Pro Tools|HD, and HD Native Systems Only)
Sets a default calibration reference level in dB when Pro Tools is in Calibration mode. For audio interfaces that have trims (such as the HD I/O), see the interface’s guide for calibration instructions.
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If your system includes one or more EUCON controllers, be sure to disable “Auto-bank to selected track” in EuControl software before enabling Pro Tools Calibration Mode to ensure that faders remain silent. To make sure “Auto-bank to select track” is not enabled, open the EuControl Settings window, click to go to the General tab, and verify the setting is not enabled. If necessary, click to disable “Auto-bank to selected track.” After exiting Calibration Mode, be sure to re-enable the “Auto-bank to selected track” setting (if necessary).
Delay Compensation Time Mode
This option lets you choose whether information in the Delay Manager is displayed in milliseconds or samples. This option is only available when Delay Compensation is enabled (Options > Delay Compensation).