diff --git a/src/genn/backends/cuda/backend.cc b/src/genn/backends/cuda/backend.cc
index 4ba6c1619a..51eab0bff3 100644
--- a/src/genn/backends/cuda/backend.cc
+++ b/src/genn/backends/cuda/backend.cc
@@ -931,7 +931,7 @@ void Backend::genInit(CodeStream &os, const ModelSpecMerged &modelMerged,
 
     // Sparse initialization kernel code
     size_t idSparseInitStart = 0;
-    if(!modelMerged.getMergedSynapseSparseInitGroups().empty()) {
+    if(!modelMerged.getMergedSynapseSparseInitGroups().empty() || !modelMerged.getMergedCustomWUUpdateSparseInitGroups().empty()) {
         os << "extern \"C\" __global__ void " << KernelNames[KernelInitializeSparse] << "()";
         {
             CodeStream::Scope b(os);
diff --git a/src/genn/backends/cuda/optimiser.cc b/src/genn/backends/cuda/optimiser.cc
index d034d473bd..3729b146bc 100644
--- a/src/genn/backends/cuda/optimiser.cc
+++ b/src/genn/backends/cuda/optimiser.cc
@@ -163,6 +163,9 @@ void calcGroupSizes(const CUDA::Preferences &preferences, const ModelSpecInterna
     // Loop through custom updates, add size to vector of custom update groups and update group name to set
     for(const auto &c : model.getCustomUpdates()) {
         groupSizes[KernelCustomUpdate].push_back(c.second.isBatched() ? (model.getBatchSize() * c.second.getSize()) : c.second.getSize());
+        if(c.second.isVarInitRequired()) {
+            groupSizes[KernelInitialize].push_back(c.second.getSize());
+        }
         customUpdateKernels.insert(c.second.getUpdateGroupName());
     }
 
@@ -186,6 +189,12 @@ void calcGroupSizes(const CUDA::Preferences &preferences, const ModelSpecInterna
                 groupSizes[KernelCustomUpdate].push_back(numCopies * sgInternal->getSrcNeuronGroup()->getNumNeurons() * sgInternal->getTrgNeuronGroup()->getNumNeurons());
             }
         }
+
+        if(c.second.isVarInitRequired()) {
+            if(sgInternal->getMatrixType() & SynapseMatrixConnectivity::SPARSE) {
+                groupSizes[KernelInitializeSparse].push_back(sgInternal->getMaxConnections());
+            }
+        }
     }
 
     // Loop through synapse groups
@@ -667,7 +676,7 @@ int chooseOptimalDevice(const ModelSpecInternal &model, KernelBlockSize &blockSi
 
     // Find ID of best device
     const int bestDeviceID = (int)std::distance(devices.cbegin(), bestDevice);
-    LOGI_BACKEND << "Optimal  device " << bestDeviceID << " - total occupancy:" << std::get<1>(*bestDevice) << ", number of small models:" << std::get<2>(*bestDevice) << ", SM version:" << std::get<0>(*bestDevice);
+    LOGI_BACKEND << "Optimal device " << bestDeviceID << " - total occupancy:" << std::get<1>(*bestDevice) << ", number of small models:" << std::get<2>(*bestDevice) << ", SM version:" << std::get<0>(*bestDevice);
 
     // Get optimal block size from best device
     blockSize = std::get<3>(*bestDevice);
diff --git a/src/genn/backends/opencl/backend.cc b/src/genn/backends/opencl/backend.cc
index 17a9416322..9a2d968f46 100644
--- a/src/genn/backends/opencl/backend.cc
+++ b/src/genn/backends/opencl/backend.cc
@@ -1181,7 +1181,7 @@ void Backend::genInit(CodeStream &os, const ModelSpecMerged &modelMerged,
 
     // Generate sparse initialisation kernel
     size_t idSparseInitStart = 0;
-    if(!modelMerged.getMergedSynapseSparseInitGroups().empty()) {
+    if(!modelMerged.getMergedSynapseSparseInitGroups().empty() || !modelMerged.getMergedCustomWUUpdateSparseInitGroups().empty()) {
         initializeKernels << "__attribute__((reqd_work_group_size(" << getKernelBlockSize(KernelInitializeSparse) << ", 1, 1)))" << std::endl;
         initializeKernels << "__kernel void " << KernelNames[KernelInitializeSparse] << "(";
         const bool anyCustomWUUpdateSparseInitGroups = !modelMerged.getMergedCustomWUUpdateSparseInitGroups().empty();