H4 updating (writing) to existing dataset.

Mostly I am working with an H4 file which already has many Datasets.
I create a copy of a Dataset with a new name or put it in a different group and I update the new dataset with new data.
I have no trouble doing this no matter how many dimensions the dataset has.

When I try to update an existing (one I did not create) 2 dimensional dataset I also have no trouble.
When I try to update an existing (one I did not create) 3 dimensional dataset I can't seem to write to it at all.

any idea what I might be doing incorrectly?

My code is: (this code works on 3D datasets I create but not on ones I don't)

private void ApplyMask(Dataset data, Dataset mask, HashMap dimtype) throws Exception
    int[] dims = (int[]) dimtype.get("dims") ;
    float fill = this.getFillValue(data);
else if (data.getRank() == 3) {
                           long maskstart[] = mask.getStartDims();
                long datastart[] = data.getStartDims();
                int x,y;
                          for (int layer = 0; layer < dims[2]; ++layer) {
                    maskstart[2] = layer ;
                    datastart[2] = layer ;
                    float[] dataRead = (float[]) data.read();
                 float[] maskRead = (float[]) mask.read();
                               for (int col = 0; col < dims[0] ; col++) {
                       for (int row = 0; row < dims[1] ; row++) {
                           x = col * dims[1] + row;
                                                    if (maskRead[x] == 1 /* mask positive value */) {
                               // leave the value there.
                               // This confirmed that we were writing values to upper layers: dataRead[x] = 44;
                           else { /* mask negative value */
                                                           if (dataRead[x] != fill ) {
                                   dataRead[x] = fill;
                   *data.write(dataRead); // this is what seems to fail - as if the permissions on the dataset if such a thing exists are not set properly.*
Debug statements in the code (left out here) confirm that up until the data.write() dataRead contains desired values.