The problem is that in the Size and Colour columns of the main product in your second CSV, you need to enter the default value of each characteristic for that product.
So it should not be:
0,Canvas Perfect Tee,,0,CA3001,1,0,1350381403,0,0,0,0,main,0,0,,0,,kg,1350383098,,m,0,0,0,0,all,,0,0,0,0,0,,0,0,,CA3001,,,"2,234",,,,,,ca3001.jpg,,,,
but:
0,Canvas Perfect Tee,,0,CA3001,1,0,1350381403,0,0,0,0,main,0,0,,0,,kg,1350383098,,m,0,0,0,0,all,,0,0,0,0,0,,0,0,,CA3001,,,"2,234",,,,,,ca3001.jpg,,,2XL ,Athletic Heather
for example.