It depends on lot of factors.
1. Whether or not you have allowed Negative Inventory in your system
2. Secondly FA calculates Avg Cost of the items when they are Received and sometimes whey they are Stocked out. That Avg Cost is saved as the Standard Cost for that item in FA. Inventory Valuation Report actually picks that Cost for Valuation.
3. Now the way that Avg Cost is calculated in FA needs to be understood. I have tried to explain this in this ARTICLE
4. There has been a lot of discussion on this topic on Forum and we are expecting some Bug Fixes in upcoming 2.5.
5. By that time if you can also share your experiences following the article above that how right or wrong you found FA to affect average cost then it will help the community.
6. There is one more way that affects Average Cost not discussed in this article because I have disabled that in PakERP. That is Location Transfers.
Hope this helps you to find more bugs and share with community and enable you to give better suggestions.