I think that your manually placed vias/routes are not being treated as power nets. The router is thinking that these are regular routes and trying to auto route them. If you used the regular power strap creation commands, then the tool would have automatically set the correct power attributes on these nets/vias. I don't know why you had to manually place via stacks instead of going through the normal pg creation flow.
Anyways check if the "route_type" attribute on these vias is "P/G strap". My suspicion is that you won't see the P/G strap attribute, which might the reason for the regular zroute to modify these.