After further investigation I found the problem.
When I query Whisper directly via the "Fetch" command it indeed got the value from the higher level as expected. When I used the render API it also worked as expected, but when I used the web-app graphs (or the API with SVG format) it did some smoothing to the graph which cause it to loose spikes. I was only able to see those spikes when I did some drill down over the period (for 2 hour resolution).
The solution is to use minXStep property for each graph and set it to 0 (0.1 will also work good enough). If you use the render API just use the minXStep property (default is 1) and if you use the Dashboards area go to "Render Options" -> "X-Axis" -> "Point-width Consolidation Threshold" and set it so some lower value than 1.
For further information see http://graphite.readthedocs.org/en/latest/render_api.html#minxstep