diff --git a/spec/package-manager-spec.coffee b/spec/package-manager-spec.coffee
index b504f676f..e6848ef03 100644
--- a/spec/package-manager-spec.coffee
+++ b/spec/package-manager-spec.coffee
@@ -154,7 +154,6 @@ describe "PackageManager", ->
 
     it "registers the config schema in the package's metadata, if present", ->
       pack = atom.packages.loadPackage("package-with-json-config-schema")
-
       expect(atom.config.getSchema('package-with-json-config-schema')).toEqual {
         type: 'object'
         properties: {
@@ -165,9 +164,20 @@ describe "PackageManager", ->
 
       expect(pack.mainModule).toBeNull()
 
+      atom.packages.unloadPackage('package-with-json-config-schema')
+      atom.config.clear()
+
+      pack = atom.packages.loadPackage("package-with-json-config-schema")
+      expect(atom.config.getSchema('package-with-json-config-schema')).toEqual {
+        type: 'object'
+        properties: {
+          a: {type: 'number', default: 5}
+          b: {type: 'string', default: 'five'}
+        }
+      }
+
     describe "when a package does not have deserializers, view providers or a config schema in its package.json", ->
       beforeEach ->
-        atom.packages.unloadPackage('package-with-main')
         mockLocalStorage()
 
       it "defers loading the package's main module if the package previously used no Atom APIs when its main module was required", ->
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index 5b0264212..6772178af 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -47,6 +47,7 @@ class PackageManager
     @packagesCache = require('../package.json')?._atomPackages ? {}
     @loadedPackages = {}
     @activePackages = {}
+    @activatingPackages = {}
     @packageStates = {}
     @serviceHub = new ServiceHub
 
@@ -62,6 +63,7 @@ class PackageManager
   reset: ->
     @serviceHub.clear()
     @deactivatePackages()
+    @loadedPackages = {}
     @packageStates = {}
 
   ###
@@ -436,9 +438,12 @@ class PackageManager
     if pack = @getActivePackage(name)
       Promise.resolve(pack)
     else if pack = @loadPackage(name)
+      @activatingPackages[pack.name] = pack
       pack.activate().then =>
-        @activePackages[pack.name] = pack
-        @emitter.emit 'did-activate-package', pack
+        if @activatingPackages[pack.name]?
+          delete @activatingPackages[pack.name]
+          @activePackages[pack.name] = pack
+          @emitter.emit 'did-activate-package', pack
         pack
     else
       Promise.reject(new Error("Failed to load package '#{name}'"))
@@ -474,6 +479,7 @@ class PackageManager
       @setPackageState(pack.name, state) if state = pack.serialize?()
     pack.deactivate()
     delete @activePackages[pack.name]
+    delete @activatingPackages[pack.name]
     @emitter.emit 'did-deactivate-package', pack
 
   handleMetadataError: (error, packagePath) ->
diff --git a/src/theme-package.coffee b/src/theme-package.coffee
index 084728869..502fbd52b 100644
--- a/src/theme-package.coffee
+++ b/src/theme-package.coffee
@@ -14,6 +14,7 @@ class ThemePackage extends Package
 
   load: ->
     @loadTime = 0
+    @configSchemaRegisteredOnLoad = @registerConfigSchemaFromMetadata()
     this
 
   activate: ->