With 4 GB in slot 1, and 2 GB in slot 3 and another 2 GB in slot 4, and IF the motherboard supports Flex mode and IF the memory controller otherwise accepts the DIMM's (capacities and chip architecture) in this configuration, then 2 GB of the 4 GB will run in dual channel mode with the 2 GB in slot 3. The remaining 2 GB of the 4 GB in slot 1 should run in single channel mode, and the 2 GB in slot 4 should also run in single channel mode.
So we should still have 4 GB in dual channel mode, plus 4 GB in single channel mode with the above configuration.
I would suggest this configuration is more stressful on the memory controller as it has to use Flex mode IF available. My configurations do not require Flex mode.
IF Flex mode is not available on this motherboard, then all of the DIMM's in the above configuration would run in single channel mode (DIMM specs and memory controller permitting). However, the OP stated having problems with running all of the DIMM's at the same time, so it is likely the DIMM specifications are not entirely compatible with the memory controller, depending on how the DIMM's are installed in the slots.