Note that the proxy does not physically modify your ini file to reflect a different value if you specify a number greater than 1000 (it only interprets such values as being something else).

If the proxy is unable to allow you to surpass the 1000 stats unit limit normally, then it does not believe that your current rate would satisfy a higher block limit. If you see that your reported block rate displayed by the proxy fluctuates greatly (perhaps due to irregular spurts in which your clients flush large number of blocks), then consider either making your clients flush more frequently. You can also try adjusting the sliding average window to encompass a larger time period, over which your sustained rate might be more indicative of "typical" activity. The last resort is to disable the intelligence with the expert mode described below.

If you read the readme, you'll see the existence of an expert mode option that will disable the intelligence regarding the 1000 stats unit threshold. However, you should be cautious in using it since you will no longer be protected from the safeguards that the limit attempts to protect you against (unknowingly fetching more blocks than you actually require).