diff --git a/.github/workflows/pr-checks.yml b/.github/workflows/pr-checks.yml
index b090a65..629d78d 100644
--- a/.github/workflows/pr-checks.yml
+++ b/.github/workflows/pr-checks.yml
@@ -40,12 +40,23 @@ jobs:
       - name: Check version pinning
         shell: bash
         run: |
-          gh codeql set-version v2.5.9
+          # Set the version without a v prefix
+          gh codeql set-version 2.5.9
           VERSION=`gh codeql version --format json | jq -r '.version'`
           if [[ $VERSION != "2.5.9" ]]; then
             echo "::error::Expected version 2.5.9 but got $VERSION"
             exit 1
           fi
+          gh codeql list-installed | grep v2.5.9
+
+          # Set the version with a v prefix
+          COUNT_BEFORE=`gh codeql list-installed | wc -l`
+          gh codeql set-version v2.5.9
+          COUNT_AFTER=`gh codeql list-installed | wc -l`
+          if [[ $COUNT_BEFORE != $COUNT_BEFORE ]]; then
+            echo "::error::Installing an already installed version changed the number of installed versions from $COUNT_BEFORE to $COUNT_AFTER!"
+            exit 1
+          fi
 
       - name: Check version unpinning
         shell: bash
@@ -56,3 +67,14 @@ jobs:
             echo "::error::Expected latest version but got 2.5.9"
             exit 1
           fi
+
+      - name: Check getting nightly version
+        shell: bash
+        run: |
+          gh codeql set-channel nightly
+          gh codeql set-version codeql-bundle-20210831-manual
+          VERSION=`gh codeql version --format json | jq -r '.version'`
+          if [[ $VERSION != "2.6.0+202108311306" ]]; then
+            echo "::error::Expected version 2.6.0+202108311306 but got $VERSION"
+            exit 1
+          fi
\ No newline at end of file
diff --git a/gh-codeql b/gh-codeql
index e3a0573..33ad90e 100755
--- a/gh-codeql
+++ b/gh-codeql
@@ -122,6 +122,10 @@ function set_version() {
     elif [ "$version" = "latest" ]; then
         version="$(gh api "repos/$repo/releases/latest" --jq ".tag_name")"
     fi
+    if [ $repo = 'github/codeql-cli-binaries' ] && [[ "$version" != v* ]] ; then
+        # Versions in github/codeql-cli-binaries have tags prefixed with v; we add this in if the user forgot.
+        version="v$version"
+    fi
     download "$version"
     gh config set extensions.codeql.version "$version"
 }
@@ -141,7 +145,7 @@ fi
 
 # Handle the list-installed command.
 if [ "$1" = "list-installed" ]; then
-    ( cd "$rootdir/dist/$channel" ; find . -depth 1 -type d | cut -c3- ; )
+    ( cd "$rootdir/dist/$channel" ; find . -mindepth 1 -maxdepth 1 -type d | cut -c3- ; )
     exit 0
 fi