I am getting this problem too. I've tried logging in and out and renaming the project and different locations on my drive, all to no success.
C:\Users\SirusAmory>butler status nsi
*errors.errorString itch.io API error: invalid target
C:/Multi-Runner/builds/58469115/0/itchio/butler/src/github.com/itchio/butler/status.go:17 (0x7e2308)
C:/Multi-Runner/builds/58469115/0/itchio/butler/src/github.com/itchio/butler/main.go:542 (0x7e625b)
C:/Multi-Runner/builds/58469115/0/itchio/butler/src/github.com/itchio/butler/main.go:445 (0x7e4e2c)
C:/Go/src/runtime/proc.go:185 (0x42a186)
C:/Go/src/runtime/asm_386.s:1629 (0x44f991)
C:\Users\SirusAmory>butler version
v5.0.1, built on May 19 2017 @ 15:51:58, ref ed26a09b37c4a0892f33d216b27e46e0650bd6cc
C:\Users\SirusAmory>