By default flot sizes the graph and axis labels to fix inside the div container. If you have a series of graphs on a page, with different variables in each graph, the sizes of the axis labels is different and the graph canvases are therefore different sizes and don’t align neatly.
Is there a way to set the size and position of the flot canvas so that the graphs are a fixed size and position within the containers
Not exactly, no. What you can do is specify how wide/high the axis labels should be, which will force the canvases to line up between different graphs.
From the API.txt:
Beyond that, if you wanted the actual axes to be the same between graphs, you would need to establish what the global min/max is for each axis between all your data sets, and then specify that for each axis in each graph.