I've built the pine ebuild with the maildir use flag, and even with specifiying folder-collections=Maildir #md/Maildir/.[] in .pinerc I the only folder I can read is my inbox. I've also downloadeed the pine sources from UW, applied the maildir patch myself and compiled it without using emerge and it works fine.
Portage 2.0.54 (default-linux/sparc/sparc64/2005.0, gcc-3.3.5-20050130, glibc-2.3.3.20040420-r2, 2.4.29-sparc sparc64) ================================================================= System uname: 2.4.29-sparc sparc64 sun4u Gentoo Base System version 1.6.14 dev-lang/python: 2.3.5-r2, 2.4.2 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.4.26-r1 ACCEPT_KEYWORDS="sparc" AUTOCLEAN="yes" CBUILD="sparc-unknown-linux-gnu" CFLAGS="-O2 -mcpu=ultrasparc" CHOST="sparc-unknown-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-O2 -mcpu=ultrasparc" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks sandbox sfperms strict" GENTOO_MIRRORS="http://gentoo.blueyonder.co.uk/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.uk.gentoo.org/gentoo-portage" USE="sparc arts avi berkdb bitmap-fonts bzip2 crypt curl dbm dlloader encode exiscan-acl expat fbcon foomaticdb fortran ftp gcc64 gd gdbm gif gmp gtk2 idn imagemagick imap imlib jpeg kde libwww mad maildir mhash mikmod motif mpeg mysql ncurses nls nocardbus oggvorbis opengl oss pam pcre pdflib perl php png readline recode sasl sdl snmp spell spf ssl tcpd tiff truetype truetype-fonts type1-fonts udev xml xml2 xv yaz zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTDIR_OVERLAY
This seems to work for me in pine 4.64 with my ~80 maildir folders.