I just stumbled across someone else who is having the same issue as me…when my Macbook wakes up from sleep I can no longer double-tap to right click. Seems petty, but it has an insane ability to piss me off. Well, knowing that someone has had to put up with the same problem, I was driven to come up with a simple fix.

Edit your crontab:

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$ crontab -e

Paste the following:

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0-59 * * * *    defaults write "Apple Global Domain" com.apple.trackpad.enableSecondaryClick 1

This will re-enable secondary clicking every minute (poor solution, but it works). If someone knows if it’s possible to trigger a script when coming out of sleep/hibernate, please let me know in the comments.