How many layers are you exporting to AXF? Since you are not exporting schema only in some cases, how many features are there in these layers? How about related tables and/or domains. After a lot of research and testing on a Recon, it became evident that RAM was the culprit for issues with our collection on 31 layers with empty schema, but domains and subtypes present. I ran the same output with everything included on a tablet with 2 GB RAM without issue and ran super fast.
My recommendation would be to eliminate any unnecessary layers (sounds like you are already doing that) or split your data into multiple AXFs/apms if feasible and use the dektop shortcuts. I split ours into two and they seemd to both work fine on the Recons. My guess is you will have better results as well with this approach. HTH