It can help if you try printing a calibration cube first - there are many of them on thingiverse.
one of the traps of 3D printing is that no two printers create an object exactly the same size, unless you spend considerable time calibrating them.
And as you found out the materials make quite a difference.
I have about 5 printers now, and each one of them is a bit different.
the short term workaround could be scaling the print. if you use something like repetier host to do the G-code, it has a feature to scale up by a percentage. Reports indicate that 2-5% is about average for PLA.
if you are really stuck, send me a message and I'll scale up the design for you.
Edit: an additional "good practice" tip with 3D printing, is to print a single part first and check the size, before wasting lots of time printing an entire project.