Stoner led team-mate Dani Pedrosa in a Honda one-two in the Netherlands last Saturday.
The result ended a run of three straight victories for Yamaha's Jorge Lorenzo, and moved Stoner into a joint championship lead with the Spaniard - Lorenzo having been taken out at the first corner by Gresini rider Alvaro Bautista.
Honda has struggled with chatter problems all season, particularly since Bridgestone changed its front tyre specification. Stoner said this was no better at Assen despite his win.
"In the past race we reduced the rear chatter but we haven't fixed it, and we haven't fixed the front," he said.
"We made a small step before the race which improved the front chatter, but for me the front tyre has no stability in it. As soon as you brake hard, it wants to fold or chatter."
The reigning MotoGP champion suspects he will never be fully comfortable with the revised tyre, though he admitted that Honda would simply have to adapt as well as it can.
"I'm still not impressed at all with the front tyre and I don't think I will be throughout the whole season," said Stoner.
"Everybody's now on the same tyre so I guess we have to find some way to make it work. But we haven't fixed any problems."
Meanwhile, Andrea Dovizioso believes he can deliver much stronger form with Tech 3 Yamaha this year than the pace that took him to the podium.
The Italian's second top-three finish of the season came after a long battle with factory Yamaha rider Ben Spies, who was ultimately slowed by tyre problems.
But Dovizioso did not feel it was one of his stronger race performances, despite the result.
"Unfortunately in the race my feeling with the front was not as good as in practice, so my lap times were slower," he said.
"My feeling with the bike in the race wasn't good enough to push 100 per cent like in other races."
Dovizioso is not sure if Tech 3 will be able to get among title protagonists and leading works riders Jorge Lorenzo, Dani Pedrosa and Casey Stoner on pure pace, but believes his team can reduce the present gap even further.
"We can go better. We can be a little bit faster. I don't know if we can fight with them, but we can be closer - and this is our target," he said.
The Assen result moved Dovizioso to within one point of team-mate Cal Crutchlow in their battle for fourth in the MotoGP championship. Dovizioso said he did not underestimate how tough the season-long fight with the Briton was going to be.
"Cal is really, really fast. Really, really fast," said Dovizioso.
"In Silverstone he was in a lot of pain but he was really fast in the race even without practice. It will be difficult to beat him, but we are there."