Changes do occur for several reasons, these being:-
1) Rod is extruded, and a high molecular weight (high viscosity) material must be used in the extrusion process so as to be able to hold the profile in the moulten state, whereas lower molecular weight (low viscosity) material is normaly used in injection moulding. High molecular weight gives improved toughness
2) Rod is extruded in a thick section, when compared to typical injection mouldings, this leads to a very slow cooling and therefore solidifying (or freezing) rate. This causes a high level of crystalisation, with the formation of large crystals. Injection moulding grades generally have a neucleating agent to increase crystalisation in the much shorter freezing times typical of injection moulding, but this grows a very large number of very small crystals.
3) The different cooling rates, and therefore crystalisation and shrinkage from the skin to the core of rod, leads to internal stresses at a level not seen in typical injection mouldings. This is exasivated by differential moisture contents accross the rod as it absorbs moisture at its surface.
4) When machineing the rod, you remove the surface layer, which is more amorphous, and has some molecular alignment in the direction fo flow.
5) When machineing the rod, you create notches which act as stress risers, increasing the chance of breakage.
6) It is rare that a machined prototype is the exact same design as the final moulded part, as the machinest generally takes a lot more time to perfect his work when making a permanent mould vs a temporary, experimental prototype. The moulded part design will normally pay attention to eliminating unnecessary material, so as to save material costs and improve cycle time, whereas, in a prototype from barstock, the machineist simply removes any material that is in the way, regards functionality of the part.
I know it is complicated, with a number of contradictions.
More details about the design and conditions of use would help in giveing a straight answer.
e-mail me direct with drawings, photo's etc if you like Regards
pat