diff --git a/cmd/showconfig.go b/cmd/showconfig.go
index 99c47b0c..d87844b2 100644
--- a/cmd/showconfig.go
+++ b/cmd/showconfig.go
@@ -37,6 +37,11 @@ func showConfig(
 	if err != nil {
 		return stackerr.NewStackErrf(err, "failed to unmarshal config")
 	}
+	log, err := logging.GetLogger(config.LogLevel)
+	if err != nil {
+		return fmt.Errorf("getting logger: %w", err)
+	}
+	ctx = log.WithContext(ctx)
 	if err := config.Initialize(ctx); err != nil {
 		return err
 	}
@@ -48,10 +53,7 @@ func showConfig(
 	if err != nil {
 		return stackerr.NewStackErrf(err, "failed to marshal yaml")
 	}
-	log, err := logging.GetLogger(config.LogLevel)
-	if err != nil {
-		panic(err)
-	}
+
 	log.Info().Msgf("Using config: %s", config.Config)
 
 	fmt.Fprintf(outputter, "%s", string(out))
diff --git a/pkg/config/config.go b/pkg/config/config.go
index 8206bcb1..7899fd9c 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -210,7 +210,11 @@ func (c *Config) getPackageConfigMap(ctx context.Context, packageName string) (m
 		return configAsMap, nil
 	}
 
-	return map[string]any{}, nil
+	// Package is something other than map, so set its value to an
+	// empty map.
+	emptyMap := map[string]any{}
+	packageSection[packageName] = emptyMap
+	return emptyMap, nil
 
 }
 func (c *Config) GetPackageConfig(ctx context.Context, packageName string) (*Config, error) {
@@ -659,6 +663,17 @@ func contains[T comparable](slice []T, elem T) bool {
 	return false
 }
 
+func deepCopyConfigMap(src map[string]any) map[string]any {
+	new := map[string]any{}
+	for key, val := range src {
+		if contains([]string{"packages", "config", "interfaces"}, key) {
+			continue
+		}
+		new[key] = val
+	}
+	return new
+}
+
 // mergeInConfig takes care of merging inheritable configuration
 // in the config map. For example, it merges default config, then
 // package-level config, then interface-level config.
@@ -684,15 +699,28 @@ func (c *Config) mergeInConfig(ctx context.Context) error {
 			pkgLog.Err(err).Msg("failed to get package config")
 			return fmt.Errorf("failed to get package config: %w", err)
 		}
+		pkgLog.Trace().Msg("got package config map")
+
 		configSectionUntyped, configExists := packageConfig["config"]
 		if !configExists {
-			packageConfig["config"] = defaultCfg
-			continue
+			pkgLog.Trace().Msg("config section doesn't exist, setting it to a deepcopy of the top-level config")
+			packageConfig["config"] = deepCopyConfigMap(defaultCfg)
 		}
+
+		pkgLog.Trace().Msg("got config section for package")
 		// Sometimes the config section may be provided, but it's nil.
 		// We need to account for this fact.
 		if configSectionUntyped == nil {
-			configSectionUntyped = map[string]any{}
+			pkgLog.Trace().Msg("config section is nil, converting to empty map")
+			emptyMap := map[string]any{}
+
+			// We need to add this to the "global" config mapping so the change
+			// gets persisted, and also into configSectionUntyped for the logic
+			// further down.
+			packageConfig["config"] = emptyMap
+			configSectionUntyped = emptyMap
+		} else {
+			pkgLog.Trace().Msg("config section is not nil")
 		}
 
 		configSectionTyped := configSectionUntyped.(map[string]any)
@@ -701,8 +729,11 @@ func (c *Config) mergeInConfig(ctx context.Context) error {
 			if contains([]string{"packages", "config"}, key) {
 				continue
 			}
+			keyValLog := pkgLog.With().Str("key", key).Str("value", fmt.Sprintf("%v", value)).Logger()
+
 			_, keyExists := configSectionTyped[key]
 			if !keyExists {
+				keyValLog.Trace().Msg("setting key to value")
 				configSectionTyped[key] = value
 			}
 		}
diff --git a/pkg/config/config_test.go b/pkg/config/config_test.go
index 580c1fb7..5a7b654e 100644
--- a/pkg/config/config_test.go
+++ b/pkg/config/config_test.go
@@ -1204,6 +1204,7 @@ with-expecter: false
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
+			ctx := context.Background()
 			tmpdir := pathlib.NewPath(t.TempDir())
 			cfg := tmpdir.Join("config.yaml")
 			require.NoError(t, cfg.WriteFile([]byte(tt.cfgYaml)))
@@ -1218,7 +1219,10 @@ with-expecter: false
 				t.Errorf("Config.Initialize() error = %v, wantErr %v", err, tt.wantErr)
 			}
 
-			cfgAsStr, err := yaml.Marshal(c._cfgAsMap)
+			cfgAsMap, err := c.CfgAsMap(ctx)
+			require.NoError(t, err)
+			
+			cfgAsStr, err := yaml.Marshal(cfgAsMap)
 			require.NoError(t, err)
 
 			if tt.wantCfgMap != "" && !reflect.DeepEqual(string(cfgAsStr), tt.wantCfgMap) {