I figured it out myself:
By transposing the matrix before writing to file, the matrices are appended as expected. Here is the working script in case anyone else experience the same issue:
fid = fopen('binFile.bin','a');
for n = 1:k
someData = rand(1000,9000);
% transpose
data = someData';
fwrite(fid,data,'double');
end
% slurp up the file with fread
bigData = fread(fid,[k*1000*9000],'double');
% reshape
bigMatrix = reshape(bigData,[k*1000, 9000]);