[Android Software/Hacking General [Developers Only]] crsklr:
I can confirm that the configuration panel shows that "disable safe-mode" is checked. So the script should be enabled.

This is the log with disable safe-mode unchecked.

v/Preparing configurations
v/Preparing configurations
v/The script is running in safe-mode!
v/The script is running in safe-mode!
v/Waiting for sdcard to initiate
v/Waiting for sdcard to initiate
v/The sdcard device was located at /dev/block/mmcblk0
v/The sdcard device was located at /dev/block/mmcblk0
v/Setting sdcard readahead to 512Kb
v/Setting sdcard readahead to 512Kb
v/Checking sdcard partitions
v/Checking sdcard partitions
v/Using /dev/block/mmcblk0p1 as fat32 (sdcard)
v/Using /dev/block/mmcblk0p1 as fat32 (sdcard)
v/Using /dev/block/mmcblk0p2 as ext4 (sd-ext)
v/Using /dev/block/mmcblk0p2 as ext4 (sd-ext)
v/Using /dev/block/mmcblk0p3 as SWAP
v/Using /dev/block/mmcblk0p3 as SWAP
v/Running file system check on sd-ext
v/Running file system check on sd-ext
e/Error detected while checking sd-ext. Everything was left uncorrected!
v/Setting optimized mount parameters on sd-ext
w/Could not mount sd-ext as ext4. Switching to auto detection!
e/The sd-ext partition could not be mounted!
v/Optimizing the internal nand partitions
v/Setting optimized mount parameters on system
v/Setting optimized mount parameters on sd-ext
v/Setting optimized mount parameters on data
v/Setting optimized mount parameters on cache
v/Looking for new system apps in /data/app-system to link to /system/app
v/The sd-ext partition was mounted successfully at /sd-ext
v/Preparing to move content between /data and /sd-ext
v/Activating SWAP partition
v/Setting swappiness value to '0'
v/Reverting /sd-ext/dalvik-cache back to /data/dalvik-cache
v/Preparing to replace the cache partition
v/Optimizing the internal nand partitions
v/Unmounting internal cache partition
v/Attaching /sd-ext/cache to /cache
v/Setting optimized mount parameters on system
v/Setting optimized mount parameters on data
v/Setting optimized mount parameters on cache
v/Looking for new system apps in /data/app-system to link to /system/app

Any ideas?

Edit: Right after hitting post, my phone buzzed me saying Mounts2SD: an error/warning was detected!". Script status is now "the sd-ext partition could not be mounted!". The log shows this now:

v/Preparing configurations
v/Preparing configurations
v/The script is running in safe-mode!
v/The script is running in safe-mode!
v/Waiting for sdcard to initiate
v/Waiting for sdcard to initiate
v/The sdcard device was located at /dev/block/mmcblk0
v/The sdcard device was located at /dev/block/mmcblk0
v/Setting sdcard readahead to 512Kb
v/Setting sdcard readahead to 512Kb
v/Checking sdcard partitions
v/Checking sdcard partitions
v/Using /dev/block/mmcblk0p1 as fat32 (sdcard)
v/Using /dev/block/mmcblk0p1 as fat32 (sdcard)
v/Using /dev/block/mmcblk0p2 as ext4 (sd-ext)
v/Using /dev/block/mmcblk0p2 as ext4 (sd-ext)
v/Using /dev/block/mmcblk0p3 as SWAP
v/Using /dev/block/mmcblk0p3 as SWAP
v/Running file system check on sd-ext
v/Running file system check on sd-ext
e/Error detected while checking sd-ext. Everything was left uncorrected!
v/Setting optimized mount parameters on sd-ext
w/Could not mount sd-ext as ext4. Switching to auto detection!
e/The sd-ext partition could not be mounted!
v/Optimizing the internal nand partitions
v/Setting optimized mount parameters on system
v/Setting optimized mount parameters on sd-ext
v/Setting optimized mount parameters on data
v/Setting optimized mount parameters on cache
v/Looking for new system apps in /data/app-system to link to /system/app
v/The sd-ext partition was mounted successfully at /sd-ext
v/Preparing to move content between /data and /sd-ext
v/Activating SWAP partition
v/Setting swappiness value to '0'
v/Reverting /sd-ext/dalvik-cache back to /data/dalvik-cache
v/Preparing to replace the cache partition
v/Optimizing the internal nand partitions
v/Unmounting internal cache partition
v/Attaching /sd-ext/cache to /cache
v/Setting optimized mount parameters on system
v/Setting optimized mount parameters on data
v/Setting optimized mount parameters on cache
v/Looking for new system apps in /data/app-system to link to /system/app
v/Executing the final steps of the script
v/Changing permissions on /data/local/tmp
v/Attaching /data/local/tmp on /sd-ext/data@local@tmp
v/Storage threshold is set to 1%

Sidenote: I'd also like to mention my appreciation for being quick to reply. Thanks a lot for the support so far!