diff --git a/Core/HLE/sceKernelMutex.cpp b/Core/HLE/sceKernelMutex.cpp
index 8a0224cb7d..bf024fbd44 100644
--- a/Core/HLE/sceKernelMutex.cpp
+++ b/Core/HLE/sceKernelMutex.cpp
@@ -215,6 +215,10 @@ void sceKernelDeleteMutex(SceUID id)
 		for (iter = mutex->waitingThreads.begin(), end = mutex->waitingThreads.end(); iter != end; ++iter)
 		{
 			SceUID threadID = *iter;
+			SceUID waitID = __KernelGetWaitID(threadID, WAITTYPE_MUTEX, error);
+			// The waitID may be different after a timeout.
+			if (waitID != id)
+				continue;
 
 			u32 timeoutPtr = __KernelGetWaitTimeoutPtr(threadID, error);
 			if (timeoutPtr != 0 && mutexWaitTimer != 0)
@@ -288,9 +292,17 @@ bool __KernelUnlockMutex(Mutex *mutex, u32 &error)
 	// TODO: PSP_MUTEX_ATTR_PRIORITY
 	bool wokeThreads = false;
 	std::vector<SceUID>::iterator iter, end;
+retry:
 	for (iter = mutex->waitingThreads.begin(), end = mutex->waitingThreads.end(); iter != end; ++iter)
 	{
 		SceUID threadID = *iter;
+		SceUID waitID = __KernelGetWaitID(threadID, WAITTYPE_MUTEX, error);
+		// The waitID may be different after a timeout.
+		if (waitID != mutex->GetUID())
+		{
+			mutex->waitingThreads.erase(iter);
+			goto retry;
+		}
 
 		int wVal = (int)__KernelGetWaitValue(threadID, error);
 		u32 timeoutPtr = __KernelGetWaitTimeoutPtr(threadID, error);
@@ -325,14 +337,6 @@ void __KernelMutexTimeout(u64 userdata, int cyclesLate)
 	if (timeoutPtr != 0)
 		Memory::Write_U32(0, timeoutPtr);
 
-	SceUID mutexID = __KernelGetWaitID(threadID, WAITTYPE_MUTEX, error);
-	Mutex *mutex = kernelObjects.Get<Mutex>(mutexID, error);
-	if (mutex)
-	{
-		// This thread isn't waiting anymore.
-		mutex->waitingThreads.erase(std::remove(mutex->waitingThreads.begin(), mutex->waitingThreads.end(), threadID), mutex->waitingThreads.end());
-	}
-
 	__KernelResumeThreadFromWait(threadID, SCE_KERNEL_ERROR_WAIT_TIMEOUT);
 }
 
@@ -543,6 +547,10 @@ void sceKernelDeleteLwMutex(u32 workareaPtr)
 		for (iter = mutex->waitingThreads.begin(), end = mutex->waitingThreads.end(); iter != end; ++iter)
 		{
 			SceUID threadID = *iter;
+			SceUID waitID = __KernelGetWaitID(threadID, WAITTYPE_LWMUTEX, error);
+			// The waitID may be different after a timeout.
+			if (waitID != mutex->GetUID())
+					continue;
 
 			u32 timeoutPtr = __KernelGetWaitTimeoutPtr(threadID, error);
 			if (timeoutPtr != 0 && lwMutexWaitTimer != 0)
@@ -631,9 +639,17 @@ bool __KernelUnlockLwMutex(NativeLwMutexWorkarea &workarea, u32 &error)
 	// TODO: PSP_MUTEX_ATTR_PRIORITY
 	bool wokeThreads = false;
 	std::vector<SceUID>::iterator iter, end;
+retry:
 	for (iter = mutex->waitingThreads.begin(), end = mutex->waitingThreads.end(); iter != end; ++iter)
 	{
 		SceUID threadID = *iter;
+		SceUID waitID = __KernelGetWaitID(threadID, WAITTYPE_LWMUTEX, error);
+		// The waitID may be different after a timeout.
+		if (waitID != mutex->GetUID())
+		{
+			mutex->waitingThreads.erase(iter);
+			goto retry;
+		}
 
 		int wVal = (int)__KernelGetWaitValue(threadID, error);
 		u32 timeoutPtr = __KernelGetWaitTimeoutPtr(threadID, error);
@@ -669,14 +685,6 @@ void __KernelLwMutexTimeout(u64 userdata, int cyclesLate)
 	if (timeoutPtr != 0)
 		Memory::Write_U32(0, timeoutPtr);
 
-	SceUID mutexID = __KernelGetWaitID(threadID, WAITTYPE_LWMUTEX, error);
-	LwMutex *mutex = kernelObjects.Get<LwMutex>(mutexID, error);
-	if (mutex)
-	{
-		// This thread isn't waiting anymore.
-		mutex->waitingThreads.erase(std::remove(mutex->waitingThreads.begin(), mutex->waitingThreads.end(), threadID), mutex->waitingThreads.end());
-	}
-
 	__KernelResumeThreadFromWait(threadID, SCE_KERNEL_ERROR_WAIT_TIMEOUT);
 }
 
diff --git a/Core/HLE/sceKernelSemaphore.cpp b/Core/HLE/sceKernelSemaphore.cpp
index ccbc46c035..b82f9f8efe 100644
--- a/Core/HLE/sceKernelSemaphore.cpp
+++ b/Core/HLE/sceKernelSemaphore.cpp
@@ -80,9 +80,13 @@ bool __KernelClearSemaThreads(Semaphore *s, int reason)
 	std::vector<SceUID>::iterator iter;
 	for (iter = s->waitingThreads.begin(); iter != s->waitingThreads.end(); ++iter)
 	{
-		SceUID threadID = *iter;
-
 		u32 error;
+		SceUID threadID = *iter;
+		SceUID waitID = __KernelGetWaitID(threadID, WAITTYPE_SEMA, error);
+		// The waitID may be different after a timeout.
+		if (waitID != s->GetUID())
+			continue;
+
 		u32 timeoutPtr = __KernelGetWaitTimeoutPtr(threadID, error);
 		if (timeoutPtr != 0 && semaWaitTimer != 0)
 		{
@@ -242,6 +246,13 @@ retry:
 		for (iter = s->waitingThreads.begin(); iter != s->waitingThreads.end(); ++iter)
 		{
 			SceUID threadID = *iter;
+			SceUID waitID = __KernelGetWaitID(threadID, WAITTYPE_SEMA, error);
+			// The waitID may be different after a timeout.
+			if (waitID != s->GetUID())
+			{
+				s->waitingThreads.erase(iter);
+				goto retry;
+			}
 
 			int wVal = (int)__KernelGetWaitValue(threadID, error);
 			u32 timeoutPtr = __KernelGetWaitTimeoutPtr(threadID, error);
@@ -288,8 +299,7 @@ void __KernelSemaTimeout(u64 userdata, int cycleslate)
 	Semaphore *s = kernelObjects.Get<Semaphore>(semaID, error);
 	if (s)
 	{
-		// This thread isn't waiting anymore.
-		s->waitingThreads.erase(std::remove(s->waitingThreads.begin(), s->waitingThreads.end(), threadID), s->waitingThreads.end());
+		// This thread isn't waiting anymore, but we'll remove it from waitingThreads later.
 		s->ns.numWaitThreads--;
 	}
 
diff --git a/Core/HLE/sceKernelThread.cpp b/Core/HLE/sceKernelThread.cpp
index c6bee53c8f..c20a70c951 100644
--- a/Core/HLE/sceKernelThread.cpp
+++ b/Core/HLE/sceKernelThread.cpp
@@ -1545,6 +1545,10 @@ void __KernelSwitchContext(Thread *target, const char *reason)
 	__KernelLoadContext(&currentThread->context);
 	DEBUG_LOG(HLE,"Context loaded (%s): %i - %s - pc: %08x", reason, currentThread->GetUID(), currentThread->GetName(), currentMIPS->pc);
 
+	// No longer waiting.
+	currentThread->nt.waitType = WAITTYPE_NONE;
+	currentThread->nt.waitID = 0;
+
 	__KernelExecutePendingMipsCalls();
 }