I guess I've just accepted it. "Belief" and "faith" are viruses that are extremely resistant to intelligence and logic. A believer can rationalize absolutely anything. In fact, the doctrinal inconsistencies, flip-flops, and personal failings of religious leaders often serve to strengthen the faith of a true believer. This is true, not just in the Watchtower/JW context, but across the religious spectrum.
Any thinking JW realizes that there are issues with JW doctrine and history. For example, lots of "spiritually strong" Witnesses believe that non-JWs will survive Armageddon. Also, many Witnesses believe that (contrary to what Jesus said in Matthew 22) they may be able to be married to their deceased spouses in the "new system." Others are skeptical about the 144k as a literal number, birthdays, and the silly rules that the WTS propagates such as no beards for men, no pantsuits for women, etc.
But these otherwise intelligent Witnesses still believe that the WTS is God's Organization. This is because they have chosen to put faith in the organization. Once you decide to put faith in something, it's over--you no longer use logic to analyze it. So, when discovering a problem with WT theology, the faithful JW does not use that fact to reconsider whether the WTS is really God's Organization. Rather, the JW figures out a way to fit this inconvenient fact into his existing belief structure--that the WTS is God's Organization.
And the constant indoctrination doesn't hurt either.