Running FatSort App in Terminal/ SD won't work in windows??

Hey Guys,
Ok I have files in folders on a sd card that I want sorted alphabetically. When I plug the sd card into my device it sorts them via when it was wrote to the card. I have tried everything. I even loaded bootcamp however there is a massive flaw with the sd card reader in windows and it won't work.I have read numerous posts online saying the SD card reader works in OSX but not Windows.. yet to find a fix for this.. I tried everything. I wish it would just work.I tried fat sort but I get errors.... can anyone help? I can not believe my iMac can't do this?

I got fat sort to partially run but errors out and I do not understand why.. I followed directions....

Jim-Richardsons-iMac-8:fatsort richardson$ diskutil unmount /dev/disk3s1
Volume SEGAGENESIS on disk3s1 unmounted
Jim-Richardsons-iMac-8:fatsort richardson$ sudo fatsort /dev/disk3s1 -c
File system: FAT32.

Sorting directory /
Sorting directory /.Spotlight-V100/
Sorting directory /.Spotlight-V100/Store-V1/
Sorting directory /.Spotlight-V100/Store-V2/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.assisted_import_post/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.assisted_import_pre/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.corespotlight/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.health_check/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.live_priority/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.live/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.live_system/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.live_user/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.migration_secondchance/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.migration/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.repair/
Sorting directory /.Spotlight-V100/Store-V2/BD353A17-37B7-4142-AAA8-B2496529DA51/journals.scan/
Sorting directory /32X/
Sorting directory /System Volume Information/
checkLongDirEntries: LongDirEntry should be marked as last long dir entry but isn't!
parseClusterChain: checkDirEntry failed in cluster 00000007 at entry 127!
sortClusterChain: Failed to parse cluster chain!
sortSubdirectories: Failed to sort cluster chain!
sortClusterChain: Failed to sort subdirectories!
sortFileSystem: Failed to sort first cluster chain!
main: Failed to sort file system!

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