You may have the situation of having multiple unrelated entities in the same Sage Intacct installation.
If you have setup each asset register separately in AssetAccountant, are you getting assets being imported to both registers instead of assets being allocated to the correct entity?
This happens because of incorrect setup.
You probably have mistakenly setup the the AA fixed asset register at the top level (company level).
You need to setup each AssetAccountant register, for each company in Sage Intacct.
This means that when you set up the integration between Sage and AssetAccountant you should choose the correct company from the drop down (not the "Top level").
If you need to fix this to receive the correct data, disconnect one of the registers from Sage Intacct (from the AssetAccountant interface > Register settings > Integrations) and then reconnect it.
You should see a choice of company, so make sure you pick the correct company, reintegrate, and retest.