Mm. Well.... Even though you describe it as a 'custom build', it still helps to know what kinda hardware you've actually got in there.
Motherboard would be good, for starters. Also, is this a USB 2.0 stick.....or a USB 3.0 variant? SanDisks can be incredibly picky about what port they're booting from.
I have an 'elderly' Compaq desktop from the early 2000s. I have a PCI-e USB 3.0 adapter card, so's I can transfer a lot of files backwards and forwards from a 3TB USB 3.0 SeaGate Expansion desktop drive at something approaching a decent speed!
I also run a lot of 'Puppies'. (That's 'Puppy' Linux.....which was originally intended to run from a USB stick.)
If I try to boot a Puppy install from a SanDisk USB 3.0 stick, plugged into the adapter card, it'll always fail.....because the card's firmware simply doesn't 'see' boot media. However, if I plug that same stick into any machine where the USB 3.0 port is native to the motherboard, it'll boot like a dream.
Hence the query about the motherboard; gives us some idea what kinda set-up you've got there, y'see.
Distros:- Multiple 'Puppies'..... and Anti-X 16.1
My Puppy BLOG ~~~ My Puppy PACKAGES
Compaq Presario SR1916UK; Athlon64 X2 3800+, 3 GB RAM, WD 500GB Caviar 'Blue', 32GB Kingspec PATA SSD, Seagate 'Expansion' 3 TB USB 3.0 external HDD, ATI Radeon Xpress 200 graphics, Dell 15.1" pNp monitor (1024 x 768), TP-Link PCI-e USB 3.0 card, Belkin PCI USB 2.0 4-port card, self-powered 7-port USB 2.0 hub
Dell Inspiron 1100; 2.6 GHz P4, 1.5 GB DDR1, 64GB KingSpec IDE SSD, Intel 'Extreme' graphics, 1 TB Seagate 'Expansion' external storage, HP HD2300 webcam.