I'm currently building a new home with 200amp service. I have requested the builder to supply 100 amp service to the rear of the home for my detached workshop. My question is a alumaflex type se cable 600 volt awg2-1 cdr awg4 the right cable? I have been told this is only rated at 65 amps? Thanks

Not sure where your getting that information, here is the spec sheet from SouthWire, that markets their version of SE cable as Alumaflex:

http://appprod.southwire.com/ProductCatalog/XTEInterfaceServlet?contentKey=prodcatsheet273

Please note the dwelling column, which means if the # 2 wire used for a residential application the ampacity is 100 amps, which is allowed by code.

If for some reason your workshop is not considered as part of the dwelling, the rating would fall under the 75 Deg C column, which is 90 amps.

Thanks for the reference and information.