A couple more bugs in --enable-multi-repl , one of which is a showstopper

Besides #1300, here are some other bugs I've hit:

### 1. I get warnings for modules "not listed in other-modules" when they are, in fact, listed in other-modules.

The false warning does not appear if I build the package or disable multi-repl.

(This one isn't a showstopper.)

### 2. "error: [GHC-39999] missing instance" for instances that definitely exist

For instance, "No instance for 'Integral Nat32'" when there is a perfectly cromulent

```
instance Integral Nat32 where ...
```

in the same module that defines Nat32.

Even better is "No instance for 'Ord FParseErr'" when

```
newtype FParseErr = GenerParseErr Text deriving (Eq, Show, Ord)
```

None of these errors appear if I use `cabal build` or load single packages into the repl.

This error makes --enable-multi-repl unusable for me.

### Info

```
$ cabal --version
cabal-install version 3.16.0.0
compiled using version 3.16.0.0 of the Cabal library (in-tree)

$ ghc --version
The Glorious Glasgow Haskell Compilation System, version 9.6.6
```

from Nixpkgs on NixOS