Can not be sure, but it looks like the same issue I had here:
Where the portal is actually taking the shards, it just isnt updating updating in your client until you let the portal close by moving away from it or going through a couple more portals then going back.
In my case I could tell it was actually taking the fuel because the amount of shards in my SS changed even though the amount in the portal appeared to not change (but actually had).
There have been multiple other similar reports that might be the same issue as well.