If you have OS 3.1 (ver 40.68) in ROM, then you should have a full 2Mb of chip mem after booting with no startup sequence.
If this is not the case, then you might have some kind of software problem with something using the memory when it shouldn't?
I think I remember trying this with my A1200 and running in to one small quirk.. That is that the buffers allocated to the various partitions (if a harddrive is present) will still eat whatever amount of memory they require. (And since there's no fast mem, it's going to go for chip.)