The system has the low throughput (37 tonnes/hour instead of 50) on top of the low operating rate (53% in the most recent week). So although not 100% sure, TEPCO thinks it's because of steel pipes clogged up with radioactive sludge. So the company is planning to bypass the particular section and see if the throughput increases.
From Jiji Tsushin via Yahoo Japan (7/23/2011):
福島第1原発事故で、東京電力は23日、高濃度の汚染水処理システムの流量が計画の毎時50トンを大幅に下回る37トン程度に減少している問題を解決する ため、内壁にのり状の汚泥が付着して流路が狭くなっている鋼鉄製配管100～200メートル分をルートから外し、ポリ塩化ビニール製ホースの「バイパス」 を設置することを明らかにした。
The contaminated water treatment system at Fukushima I Nuclear Power Plant has been suffering from the lower than designed throughput of 37 tonnes per hour instead of 50. On July 23, TEPCO disclosed a plan to create a 'bypass" using a PVC hose to divert the flow from going through 100 to 200 meters of steel pipes which are clogged with the sludge.
The company measured the radiation on the surface of the steel pipes in preparation of the work, and the radiation was high at 50 millisieverts/hour. TEPCO is considering how to proceed in the high radiation condition.
I think the PVC hose TEPCO is planning to use is an orange-colored hose that has been used throughout the plant, called "Kanaflex", which had an unfortunate rupture the other day.
Since TEPCO hasn't released the "survey map" (contamination map) of the plant since June 24, I don't know which pipe segment that TEPCO is talking about. The June 24 map shows the surface radiation of the pipes that transfer the contaminated water all exceeds 100 millisieverts/hour and as high as 210 millisieverts/hour.