House of GVSB, major label signing, Freak*on*ica, and label shifts (1996–2000)
The band focused on creating their subsequent album in the latter half of 1995, again with Niceley as producer. House of GVSB was released in March 1996 and was critically praised by numerous outlets such as Spin (which ranked the album at No. 5 on its Best Albums of 1996 list), Kerrang, Sounds, and others. House of GVSB also appeared on the UK Albums Chart at No. 76. "Super-Fire" was released as the lead single, and it peaked at No. 82 on the UK Singles Chart, the band's highest position on the chart (it also peaked at No. 36 on the UK Dance Singles Chart). They performed the track on the television shows 120 Minutes (along with the other House of GVSB single "Disco Six Six Six") and Nulle Part Ailleurs in 1996. They also toured with Therapy? and Rage Against the Machine during the first half of 1996. For the second half of 1996, they joined the Lollapalooza tour for the third and final time. They also appeared at two prominent festivals in 1996, HFStival in Washington, D.C., and Reading in England. The 1996 film Suburbia contained Girls Against Boys' track "Bullet Proof Cupid" (originally from Venus Luxure No. 1 Baby) on its soundtrack. During the band's 1996 tours, they embraced various electronica and industrial acts. Janney took a side job as a DJ in New York City during 1997 to experiment with various sounds. He also remixed for numerous artists such as Sneaker Pimps and Ruby. Overall, the events became an early indication of the band's follow-up album. The group played a small number of shows throughout 1997, including the inaugural Fuji Rock Festival in Japan during the 1997 Pacific typhoon season. Also in 1997, the band's song "Super-Fire" from the House of GVSB album appeared in the film Love God. Spin also listed Girls Against Boys at No. 38 on its annual Most Vital Artists list.
Numerous major labels approached Girls Against Boys, but the band initially resisted the labels' overtures, wanting to fulfill their three-album deal with Touch and Go. According to McCloud, their decision to stick with Touch and Go "only made the majors go more crazy for us," and soon "all the labels were following us around, buying us rooms in 5 star hotels, which was crazy, because we were still playing punk rock squats in Italy, for instance." Former Girls Against Boys guitarist Wood, who by then was working as an executive at Geffen Records, reached out to the band on behalf of his employer. The band signed a three-album deal with Geffen, and started recording their major label debut with producer Nick Launay in October 1997.
The recording process was deemed to be exhaustive because production lasted nearly six months. Previously, the band spent only one or two months on production. The electronic-influenced album Freak*on*ica was released in June 1998. The album peaked at No. 11 on the Billboard Heatseekers Chart and at No. 182 on the UK Albums Chart. It was praised by various publications such as Entertainment Weekly, Spin, and Pitchfork; however, it was criticized by other publications such as Rolling Stone and The A.V. Club. "Park Avenue" was released as the lead single, and it peaked at No. 83 on the UK Singles Chart and at No. 28 on the Billboard Hot Mainstream Rock Tracks chart. "Psycho-Future" from Freak*on*ica was released as a single as it appeared on the soundtrack to the 1998 remake film Psycho. The band went on a headlining tour throughout 1998, followed by a tour with labelmates Garbage. They also played at the Reading festival in England and Pukkelpop in Belgium. Girls Against Boys appeared on Late Night With Conan O'Brien, performing "Park Avenue". The band contributed the song "EPR" to the soundtrack of the film Permanent Midnight, and they appeared in the film 200 Cigarettes in one scene. Their cover of "Boogie Wonderland" was included on the 200 Cigarettes soundtrack.
Although Freak*on*ica performed moderately well (it was the band's best-selling effort up to that point), it did not meet Geffen Records' sales expectations. After the album's release, Geffen was bought by Canadian multinational Seagram. According to McCloud, Girls Against Boys were informed during their tour with Garbage "that Geffen Records would cease to exist as of January 1, 1999," leaving the band's future uncertain.
After a short 1999 tour with Firewater, Girls Against Boys remained in limbo as Universal Records (the parent of Geffen Records) continued to restructure its business, and the band was unable to extensively record or tour for nearly two years. Also in 1999, two tracks from Freak*on*ica ("Park Avenue" and "Psycho-Future") appeared in the racing video game Test Drive Off-Road 3. Girls Against Boys began demoing songs for a new album, initially slated to be released in early 2000. At one point that year, the band was moved to the Interscope Records brand; however, various conflicts led to the band parting ways with the label.