Election results from Texas’ largest county were delayed for hours. What happened?

A last-minute change in how votes were counted threw Harris County into an electoral muddle Tuesday, causing nearly 12-hour delays in results for the closely watched mayor's race and a raft of state constitutional amendments.

While exasperating election night vigils are not unusual in the state's largest county, this election's prolonged delay raised questions about what went wrong and why it took hours to make even a fraction of tallies public.

In past elections, results from individual precincts were taken to several drop-off locations around the county, which fed the tallies to the central office. This time, however, the electronic ballot cards with vote counts from individual precincts had to be driven from polling sites — some of them nearly 40 minutes away; some still running an hour after polls closed — into downtown Houston for tallying to begin. Just a quarter of returns had been reported right before midnight. A complete set didn't come in until nearly 7 a.m. Wednesday.

“This was a painstakingly manual process that amounted to only one person processing [results] cards at a time where we could have had one person at each of the 10 drop off locations submitting electronically with our original plan,” Diane Trautman, the Harris County clerk, said in an email Wednesday morning. “The contingency plan we were forced to use was only meant to be used in case of natural disaster or power outage.”

The county switched to the more cumbersome process after an election advisory issued by the Texas Secretary of State’s Office days into the early voting period forced it to ditch its usual practice of sending returns to “rally stations” throughout the county to be downloaded.

Harris County had used a similar system for years, plugging memory cards, known as “mobile ballot boxes,” into specific readers at the rally stations and transmitting the vote tallies to a central office through a secure phone line, according to county officials. As it had in the May municipal election, the county was planning to use a secure encrypted internal network this time around.

But citing security worries, the secretary of state’s advisory required the county to make copies of those memory cards if it wanted to transmit the data over encrypted lines. The originals could be processed directly at the main office.

Though the advisory was issued on Oct. 23, election officials in Harris and other counties said they weren’t made aware of it until several days later. By then, county officials said, it was too late for the county to purchase the equipment needed to make copies.

“We could’ve done that if there had been more than 13 days warning,” said Douglas Ray, a special assistant county attorney in Harris County. “It was just too short a period of time to get from point A to point B and pull this off in the way we intended to do it.”

Instead, the county turned to a contingency plan that included law enforcement escorts transporting ballot box memory cards from each polling site to the central counting station. The effort was further delayed when more than half of the county’s 757 polling places were still running at 8 p.m. as voters who were in line when polls closed finished casting their ballots.

In the aftermath of the Election Day mayhem, Harris County officials said they plan to get technology in place to resume using "rally stations" in the next election. They wonder why the secretary of state’s decided this year to object to a process long in place.

Ray says Keith Ingram, the state's director of elections, told county attorneys during a conference call this week that Harris County's procedures have actually been out of compliance with state law for a decade. Ray said state officials told him and other lawyers on the call that the secretary of state's office was "compelled to issue" its advisory ahead of Tuesday's election after facing external pressure from the Harris County GOP.

A spokesman for the secretary of state’s office did not respond to questions about the Monday conference call but did provide an email he sent to state Sen. Carol Alvarado in which Ingram wrote that the intranet connection Harris County was switching to wasn't in compliance with state law and was never approved by the secretary of state's office.

"Directly connecting the county’s voting system to the intranet would have eliminated the protections that an air-gapped system provides and subjected the county to major security risks," Ingram wrote.

Ingram also said his office included the language in the advisory that prompted Harris County's last-minute change without anticipating "any adverse impact" because the secretary of state's office had already spoken with the county election officials who were made aware of the need to make copies of the memory cards.

A spokeswoman for the Harris County GOP said the party did not communicate with the secretary of state's office until last Thursday.

But the party has raised concerns about the county clerk's planned use of an encrypted internal network, arguing that the connection would not comply with state law.

“It is unfortunate that Clerk Trautman has rushed out her agenda by implementing a system not ready for prime time, and despite the law,” said Paul Simpson, Harris County Republican Party Chairman, in a written statement.