Linux Mint 18 (based on Ubuntu Xenial), F# 4.1, .Net Core 2.1.4. To reproduce:
dotnet new mini-scaffold -n MyCoolNewLib -lang F#
cd MyCoolNewLib
./build.sh
Result: Paket restore did not restore packages/build/FAKE/tools/FAKE.exe, so the build naturally failed.
BTW, when I ran mono .paket/paket.exe -v restore, Paket said, "Last restore is still up to date". So this might be a Paket bug; I'm still trying to track down why Paket thinks the last restore is still up to date when there's no packages folder at all.