They got better as time went on but it really took a number of years before people could get reasonably high-performance, reliable PCI implementations. For x86, aside from AMD's Irongate (750/760) chipsets (K7-era) and nVidia (nForce), pretty much only Intel had PCI working reasonably. ALI, VIA and SiS PCI implementations always had weird issues and quirks.
PCI-IDE adapters are another good example -- VIA's PCI IDE had all sorts of issues, if you wanted high performance PCI IDE, it worked best with Intel.
It's not that different with modern PCIe-SATA either (history repeats), Marvell PCIe/SATA adapters have lingering oddities.