This is probably a performance issue with the jGraph library that jMemorize uses for charting and reporting.
I use jMemorize over a Core Duo 2.3MH, 1GB RAM, ubuntu 10.4 machine.
I have a jml file which contains 900+ cards and I've been using jMemorize for 2 years for memorizing them. So a significant percentage of cards are in deck 9 and 10.
When I start reviewing cards, I can easily feel the time that jMemorize needs to redraw the chart. It takes almost a second to redraw the chart and show the next card when I click on the "Yes" (on "No") button. If I make the chart invisible, jMemorize shows the next card almost instantaneously when I click on the "Yes" button.