The tolled roads in Wallonia are managed by an independent public entity with a VAT system called Sofico. Therefore, the Sofico invoice contains VAT for the trips made on Sofico roads.
The (fleet) tax statements of the Flemish Region and the Brussels-Capital Region are issued by the government, which is why there is no VAT.

IMPORTANT! You can recuperate the VAT on the Sofico invoices (for Wallonia). 

Please note that the toll is 100% deductible and that the Belgian VAT refund for 2017 can be claimed until 30/09/2018 by non-Belgian companies. For more information, please check with your accountant.